Miracle-dz/UniFAR-FTUs huggingface dataset:
Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures

The initial step in HIV-1 infection occurs with the binding of cell surface CD4 to trimeric HIV-1 envelope glycoproteins (Env), a heterodimer of a transmembrane glycoprotein (gp41) and a surface glycoprotein (gp120). The design of soluble versions of trimeric Env that display structural and functional properties similar to those observed on intact viruses is highly desirable from the viewpoint of designing immunogens that could be effective as vaccines against HIV/AIDS. Using cryoelectron tomography combined with subvolume averaging, we have analyzed the structure of SOSIP gp140 trimers, which are cleaved, solubilized versions of the ectodomain of trimeric HIV-1 Env. We show that unliganded gp140 trimers adopt a quaternary arrangement similar to that displayed by native unliganded trimers on the surface of intact HIV-1 virions. When complexed with soluble CD4, Fab 17b, which binds to gp120 at its chemokine coreceptor binding site, or both soluble CD4 and 17b Fab, gp140 trimers display an open conformation in which there is an outward rotation and displacement of each gp120 protomer. We demonstrate that the molecular arrangements of gp120 trimers in the closed and open conformations of the soluble trimer are the same as those observed for the closed and open states, respectively, of trimeric gp120 on intact HIV-1 BaL virions, establishing that soluble gp140 trimers can be designed to mimic the quaternary structural transitions displayed by native trimeric Env.
Effects of Sample Size in Classifier Design

The effect of finite sample-size on parameter estimates and their subsequent use in a family of functions are discussed. General and parameter-specific expressions for the expected bias and variance of the functions are derived. These expressions are then applied to the Bhattacharyya distance and the analysis of the linear and quadratic classifiers, providing insight into the relationship between the number of features and the number of training samples. Because of the functional form of the expressions, an empirical approach is presented to enable asymptotic performance to be accurately estimated using a very small number of samples. Results were experimentally verified using artificial data in controlled cases and using real, high-dimensional data. >
Effects of Exercise Training on Endothelial Progenitor Cells in Cardiovascular Disease: A Systematic Review

ABSTRACTThis review aimed to examine the effects of exercise training on mobilization of endothelial progenitor cells (EPCs) in patients with cardiovascular disease and to discuss the possible mechanisms involved in the process. A computer-aided search on PubMed and PEDro was conducted to identify relevant studies published up to June 2012. Two reviewers independently selected studies for inclusion and extracted data, namely, quantitative assessment of circulating EPCs. Of the 88 identified studies, 13 met the inclusion criteria. The 13 studies enrolled 648 participants, including patients with chronic heart failure, peripheral artery disease, and coronary artery disease. The exercise characteristics varied largely across the studies: exercise duration ranged from 2 wks to 6 mos, session duration ranged from 20 to 60 mins, and exercise intensity was usually calculated using the maximal heart rate (ranging from 75% to 85%) or the peak/maximum oxygen consumption (60%–70%). All studies used aerobic exercise. The great majority of the 13 studies reported significant effects of different exercise regimens on the number of circulating EPCs. In summary, exercise training seems to increase the number of circulating EPCs, which could contribute to vascular regeneration and angiogenesis. These positive effects of chronic exercise seem to be closely related to the bioavailability of nitric oxide, including increased activity of endothelial nitric oxide synthase and antioxidant enzymes, and activation of matrix metalloproteinase 9.
Higher sensitivity troponin assays: Quo vadis?

Central to the universal definition of myocardial infarction (MI) is the recommendation that cardiac troponin (cTn; I or T) is the biomarker of choice for detection of myocardial necrosis because of its high clinical sensitivity and almost absolute myocardial tissue specificity.1 The guidelines are based on the assays presently available for clinical use. However, predicated on data suggesting that there is additional information below the levels that are presently being measured, manufacturers have begun to develop much more sensitive cTn assays that allow measurement of concentrations in the range of pg/ml rather than ng/ml. These assays should permit accurate measurement of most if not all normal subjects with an optimal level of analytical imprecision (coefficient of variation ≤10%). Preliminary observations using levels now measurable and based on values below the present 99th percentile of the current assays suggest that more sensitive assays will result in an increased diagnosis of MI and that these patients are at substantial risk post-infarction.2 Recent data indicate that these previously undetectable levels are also associated with worse outcomes in patients with an acute coronary syndrome,2 especially if these low level elevations continue post-event,3 in those with heart failure,4 and stable angina pectoris,5 and even elderly apparently healthy population cohorts.6,7 These concentrations have also been found to be associated with cardiovascular high-risk features, higher carotid artery plaque burden, and … *Corresponding author. Tel: +45 89497614, Fax: +45 89497619, Email: Kristian.Thygesen{at}as.aaa. dk; or kthygesen{at}oncable.dk
The potential use of lures for thrips biological control in greenhouses: practice and theory

Exploiting the response of thrips pest species to odours has long been a goal for improving thrips pest management including biological control. Applications of attractants could include improved monitoring, push-pull (in conjunction with a repellent odour), lure and kill, and lure and infect technologies, and surveillance for invasive organisms. We have recently discovered that 4-pyridyl carbonyl compounds can elicit responses from a range of thrips species (Thrips tabaci, T. major, T. obscuratus and Frankliniella occidentalis) in the laboratory, in glasshouses and in open field bioassays. Some of these compounds can increase the trap capture of these thrips species in both commercial greenhouses and broad acre commercial crops where these species are considered pests. However, our understanding of the mechanisms eliciting this response in thrips is still only rudimentary. Greater knowledge of the underlying behavioural mechanisms, including the intrinsic and extrinsic factors that may affect these responses, as well as optimal trap design and configuration, and odour formulation, will be essential if semiochemical-based approaches are to be integrated into thrips management programmes
Gastric Precancerous Lesions and Helicobacter pylori Infection in Relatives of Gastric Cancer Patients from Northeastern Brazil

Background: Helicobacter pylori infection predisposes to gastric cancer. First-degree relatives of patients with gastric cancer have an increased risk of developing the disease. Aim: To evaluate the prevalence of gastric precancerous gastric lesions and H. pylori infection in first-degree relatives of non-cardia gastric cancer patients. Methods: Gastric cancer relatives (n = 104) from a region with high prevalence of H. pylori infection and gastric cancer were invited for screening endoscopy; 80% of them had dyspeptic symptoms. The control group was composed of patients (n = 118) who concurrently underwent upper gastrointestinal endoscopy for investigation of dyspepsia with no family history of gastric cancer. The groups were matched for gender, age and social class. H. pylori status was evaluated by urease test, and histology and histological parameters were assessed according to the Houston Updated Sydney System. Results: The prevalence of H. pylori infection was high in both the relative (84.7%) and the control (75.9%) groups. Corpus-predominant gastritis was more frequently observed in the relative group, whereas antral gastritis predominated in the controls. The density of lymphoid follicles was higher among the relatives. Also, intestinal metaplasia in the corpus and dysplasia were more prevalent in the cancer relative group than in the control group. Early gastric cancer was detected in 1 relative of gastric cancer patient with high-grade dysplasia. Conclusion: Individuals with a family history of non-cardia gastric cancer need to be routinely screened for H. pylori infection and precancerous gastric lesions.
Sequential decoding with trellis shaping

Sequential decoding of the channel code in a trellis-coded modulation system with trellis shaping can be used to reduce the system complexity and to achieve high coding gain with large constraint-length codes. It is shown that almost all the shaping gain that can be achieved when Viterbi decoding is used for the channel code can also be achieved when sequential decoding is used for the channel code. It is also shown that the real shaping gain is a function of both the SNR and the spectral efficiency.
Disseminated nocardiosis in a patient on infliximab and methylprednisolone for treatment-resistant Sweet's syndrome

A 62-year-old white man with a 10-year history of treatment-refractory Sweet's syndrome was admitted to the hospital with the onset of purpuric lesions. Methylprednisolone and infliximab were administered. Our patient developed disseminated Nocardia infection and eventually succumbed. Opportunistic infections such as Nocardia have been associated with infliximab and other tumour necrosis factor (TNF)-α inhibitors. The astute clinician should be aware of the risk of rare opportunistic infections, particularly in patients on TNF-α inhibitors and systemic corticosteroids.
Supplementary Information to the paper in J. R. Soc. Interface “Model Predictions of Deformation, Embolization, and Permeability of Partially Obstructive Blood Clots under Variable Shear Flow”

Energetic Variational Approach (EnVarA), based on the first and second laws of thermodynamics, is grew out of the seminal work of Lars Onsager [10, 11]. The EnVarA has been extensively used to model complex fluid systems [9]. The general framework of the EnVarA is based on the combination of the statistical physics and nonlinear thermodynamics. The Least Action Principle (LAP) is applied to the Hamiltonian part of the energy functional to obtain conservative force. The Maximum Dissipation Principle (MDP) is used to obtain the dissipative force. The final equation of motion is obtained by balancing conservative and dissipative forces. The total energy functional Etot of the system used for modeling deformation of already formed blood clot, combines macroscopic kinetic energy Ekin, which arises from the macroscopic flow, and microscopic energy, consisting of the elastic energy Eela and the mixing energy Ecoh representing interactions between different phases:
Emotional Voice and Emotional Body Postures Influence Each Other Independently of Visual Awareness

Multisensory integration may occur independently of visual attention as previously shown with compound face-voice stimuli. We investigated in two experiments whether the perception of whole body expressions and the perception of voices influence each other when observers are not aware of seeing the bodily expression. In the first experiment participants categorized masked happy and angry bodily expressions while ignoring congruent or incongruent emotional voices. The onset between target and mask varied from −50 to +133 ms. Results show that the congruency between the emotion in the voice and the bodily expressions influences audiovisual perception independently of the visibility of the stimuli. In the second experiment participants categorized the emotional voices combined with masked bodily expressions as fearful or happy. This experiment showed that bodily expressions presented outside visual awareness still influence prosody perception. Our experiments show that audiovisual integration between bodily expressions and affective prosody can take place outside and independent of visual awareness.
Context Representation and Fusion: Advancements and Opportunities

The acceptance and usability of context-aware systems have given them the edge of wide use in various domains and has also attracted the attention of researchers in the area of context-aware computing. Making user context information available to such systems is the center of attention. However, there is very little emphasis given to the process of context representation and context fusion which are integral parts of context-aware systems. Context representation and fusion facilitate in recognizing the dependency/relationship of one data source on another to extract a better understanding of user context. The problem is more critical when data is emerging from heterogeneous sources of diverse nature like sensors, user profiles, and social interactions and also at different timestamps. Both the processes of context representation and fusion are followed in one way or another; however, they are not discussed explicitly for the realization of context-aware systems. In other words most of the context-aware systems underestimate the importance context representation and fusion. This research has explicitly focused on the importance of both the processes of context representation and fusion and has streamlined their existence in the overall architecture of context-aware systems’ design and development. Various applications of context representation and fusion in context-aware systems are also highlighted in this research. A detailed review on both the processes is provided in this research with their applications. Future research directions (challenges) are also highlighted which needs proper attention for the purpose of achieving the goal of realizing context-aware systems.
Patterns of diagnosis and therapeutic care of epilepsy at a tertiary referral center in Nigeria

Epilepsy care in developing countries is challenged by the paucity of trained specialists, diagnostic tools, and antiepileptic drugs (AEDs). We retrospectively evaluated how epilepsy was managed in a Nigerian tertiary referral center, with the goals of determining diagnostic accuracy by comparing clinical and electroencephalography (EEG) diagnoses, the appropriateness of prescribed therapy by clinician specialization, and the association between therapy and patient outcomes.
Internet Addiction and Modeling its Risk Factors in Medical Students, Iran

Background: Today's internet is a usual and common method for identifying and fulfilling unknown practices. Internet network has been prepared rapid and comfortable access to information. Internet addiction is a new and attractive subject that has been regarded as behavior-based addiction recently. Purpose: To estimate the prevalence of internet addiction and some of the related factors among medical students, Iran. Materials and Methods: An analytical cross-sectional study was conducted on 426 students selected through two-stage sampling method. Yang standard internet addiction questionnaire was used for data collection. After data entry, χ2, t-test, and Pearson coefficient statistical tests were applied. 0.05 was considered as the significance level. Results: The overall prevalence of internet addiction was 10.8%, with moderate and severe internet addiction equal to 8% and 2.8%, respectively. Mean and standard deviation of Yang internet addiction score was calculated as 32.74±14.52. Internet addiction was associated with sex, marital status, father's job, rate of knowledge about computer and internet, and educational level (P<0.05). But it was not associated with the parents’ education, residential area, field of study and level, and school of education (P>0.05). Conclusion: Because internet addiction leads to wasting of the students’ leisure time and also useful time, it affects the educational situation inversely. Some measures should be taken to plan and improve the use of internet.
Conjugated Linoleic Acid and Disease Prevention: A Review of Current Knowledge

Conjugated linoleic acid (CLA), a derivative of a fatty acid linoleic acid (LA), has been reported to decrease tumorigenesis in animals. CLA is unique because unlike most antioxidants which are components of plant products, it is present in food from animal sources such as dairy foods and meats. CLA concentrations in dairy products typically range from 2.9 to 8.92 mg/g fat of which the 9-cis, 11-trans isomer makes up to 73% to 93% of the total CLA. Low concentrations of CLA are found in human blood and tissues. In vitro results suggest that CLA is cytotoxic to MCF-7 cells and it inhibits the proliferation of human malignant melanoma and colorectal cancer cells. In animal studies, CLA has inhibited the development of mouse epidermal tumors, mouse forestomach cancer and rat mammary cancer. Hamsters fed CLA collectively had significantly reduced levels of plasma total cholesterol, non-high-density lipoprotein cholesterol, (combined very-low and low-density lipoprotein) and triglycerides with no effect on high-density lipoprotein cholesterol, as compared to controls. Dietary CLA modulated certain aspects of the immune defense but had no obvious effect on the growth of an established, aggressive mammary tumor in mice. It is now thought that CLA itself may not have anti-oxidant capabilities but may produce substances which protect cells from the detrimental effects of peroxides. There is, however, insufficient evidence from human epidemiological data, and very few of the animal studies have shown a dose-response relationship with the quantity of CLA feed and the extent of tumor growth. Further research with tumor models is needed to test the efficacy and utility of CLA in cancer and other disease prevention and form the basis of evaluating its effect in humans by observational studies and clinical trials.
Circulating Retinol-Binding Protein-4, Insulin Sensitivity, Insulin Secretion, and Insulin Disposition Index in Obese and Nonobese Subjects

OBJECTIVE Recent investigations disclosed an upregulation of retinol-binding protein-4 (RBP4) in the adipose tissue of several insulin-resistant mouse models and increased serum RBP4 concentration in subjects with obesity and type 2 diabetes in association with insulin resistance. There is some experimental evidence that RBP4 also could been linked to insulin secretion. RESEARCH DESIGN AND METHODS We aimed to evaluate insulin secretion, insulin sensitivity, insulin disposition index (minimal model analysis), and circulating RBP4 (enzyme-linked immunosorbent assay) in nondiabetic men with a wide range of obesity (n = 107). RESULTS Serum RBP4 concentration was nonsignificantly different among lean, overweight, and obese subjects. Circulating RBP4 was not associated with age, BMI, waist-to-hip ratio, or metabolic parameters, including insulin sensitivity (r = -0.03, P = 0.6). On the contrary, circulating RBP4 was negatively associated with insulin secretion, especially in obese subjects (r = -0.48, P = 0.007), in whom RBP4 also was linked to insulin disposition index (r = -0.44, P = 0.01). On multiple regression analyses to predict insulin secretion (acute insulin response [AIR(g)]), insulin sensitivity was the only factor that contributed to 17% of AIR(g) variance in nonobese subjects. In obese subjects, however, RBP4 emerged as an independent factor that contributed independently to AIR(g) variance (23%). CONCLUSIONS Our results suggest that oversecretion of RBP4 may negatively affect beta-cell function directly or by preventing the binding of transthyretin to its receptor. These mechanisms could be behind the association between increased circulating RBP4 and type 2 diabetes. RBP4 could be one signal from insulin-resistant tissues that impacts on beta-cell secretion.
WDM network optimization by ILP based on source formulation

Efficient planning and optimization of wavelength division multiplexing networks is an important issue today. Integer linear programming (ILP) is the most used exact method to perform this task. We propose a new ILP formulation that allows to solve optimization with less computational effort compared to other ILP approaches. This formulation applies to multifiber mesh networks with or without wavelength conversion, when either the total fiber number or the total fiber length is the cost function to be minimized. After presenting the formulation we discuss the results we obtained by exploiting it in the optimization of two case-study networks.
Learning Closed Horn Expressions

The paper studies the learnability of Horn expressions within the framework of learning from entailment , where the goal is to exactly identify some pre-fixed and unknown expression by making queries to membership and equivalence oracles. It is shown that a class that includes both range restricted Horn expressions (where terms in the conclusion also appear in the condition of a Horn clause) and constrained Horn expressions (where terms in the condition also appear in the conclusion of a Horn clause) is learnable. This extends previous results by showing that a larger class is learnable with better complexity bounds. A further improvement in the number of queries is obtained when considering the class of Horn expressions with inequalities on all syntactically distinct terms.
Agonist- and Ca2+-dependent Desensitization of TRPV1 Channel Targets the Receptor to Lysosomes for Degradation*

Background: The contribution of TRPV1 trafficking to vanilloid-induced desensitization and tachyphylaxis remains unexplored. Results: Agonist exposure promotes TRPV1 internalization and degradation in nociceptors and HEK293 cells, in a time-, dose-, and Ca2+-dependent manner. Conclusion: Agonist-induced TRPV1 internalization and degradation notably contribute to long-term nociceptor desensitization. Significance: Modulation of surface TRPV1 levels could be a therapeutic approach for pain treatment. TRPV1 receptor agonists such as the vanilloid capsaicin and the potent analog resiniferatoxin are well known potent analgesics. Depending on the vanilloid, dose, and administration site, nociceptor refractoriness may last from minutes up to months, suggesting the contribution of different cellular mechanisms ranging from channel receptor desensitization to Ca2+ cytotoxicity of TRPV1-expressing neurons. The molecular mechanisms underlying agonist-induced TRPV1 desensitization and/or tachyphylaxis are still incompletely understood. Here, we report that prolonged exposure of TRPV1 to agonists induces rapid receptor endocytosis and lysosomal degradation in both sensory neurons and recombinant systems. Agonist-induced receptor internalization followed a clathrin- and dynamin-independent endocytic route, triggered by TRPV1 channel activation and Ca2+ influx through the receptor. This process appears strongly modulated by PKA-dependent phosphorylation. Taken together, these findings indicate that TRPV1 agonists induce long-term receptor down-regulation by modulating the expression level of the channel through a mechanism that promotes receptor endocytosis and degradation and lend support to the notion that cAMP signaling sensitizes nociceptors through several mechanisms.