Miracle-dz/UniFAR-FTUs huggingface dataset:
Network Coding-Based Broadcast in Mobile Ad-hoc Networks

Broadcast operation, which disseminates information network-wide, is very important in multi-hop wireless networks. Due to the broadcast nature of wireless media, not all nodes need to transmit in order for the message to reach every node. Previous work on broadcast support can be classified as probabilistic (each node rebroadcasts a packet with a given probability) or deterministic approaches (nodes pre-select a few neighbors for rebroadcasting). In this paper, we show how network-coding can be applied to a deterministic broadcast approaches, resulting in significant reductions in the number of transmissions in the network. We propose two algorithms, that rely only on local two-hop topology information and makes extensive use of opportunistic listening to reduce the number of transmissions: 1) a simple XOR-based coding algorithm that provides up to 45% gains compared to a non-coding approach and 2) a Reed-Solomon based coding algorithm that determines the optimal coding gain achievable for a coding algorithm that relies only on local information, with gains up to 61% in our simulations. We also show that our coding-based deterministic approach outperforms the coding-based probabilistic approach presented in (C. Fragouli et al, 2006).
I(FIB)F: Iterated bloom filters for routing in named data networks

Named Data Networks provide a clean-slate redesign of the Future Internet for efficient content distribution. Because Internet of Things are expected to compose a significant part of Future Internet, most content will be managed by constrained devices. Such devices are often equipped with limited CPU, memory, bandwidth, and energy supply. However, the current Named Data Networks design neglects the specific requirements of Internet of Things scenarios and many data structures need to be further optimized. The purpose of this research is to provide an efficient strategy to route in Named Data Networks by constructing a Forwarding Information Base using Iterated Bloom Filters defined as I(FIB)F. We propose the use of content names based on iterative hashes. This strategy leads to reduce the overhead of packets. Moreover, the memory and the complexity required in the forwarding strategy are lower than in current solutions. We compare our proposal with solutions based on hierarchical names and Standard Bloom Filters. We show how to further optimize I(FIB)F by exploiting the structure information contained in hierarchical content names. Finally, two strategies may be followed to reduce: (i) the overall memory for routing or (ii) the probability of false positives.
A simple and inexpensive point-of-care test for hepatitis B surface antigen detection: serological and molecular evaluation

Early identification of chronic hepatitis B is important for optimal disease management and prevention of transmission. Cost and lack of access to commercial hepatitis B surface antigen (HBsAg) immunoassays can compromise the effectiveness of HBV screening in resource‐limited settings and among marginalized populations. High‐quality point‐of‐care (POC) testing may improve HBV diagnosis in these situations. Currently available POC HBsAg assays are often limited in sensitivity. We evaluated the NanoSign® HBs POC chromatographic immunoassay for its ability to detect HBsAg of different genotypes and with substitutions in the ‘a’ determinant. Thirty‐seven serum samples from patients with HBV infection, covering HBV genotypes A–G, were assessed for HBsAg titre with the Roche Elecsys HBsAg II quantification assay and with the POC assay. The POC assay reliably detected HBsAg at a concentration of at least 50 IU/mL for all genotypes, and at lower concentrations for some genotypes. Eight samples with substitutions in the HBV ‘a’ determinant were reliably detected after a 1/100 dilution. The POC strips were used to screen serum samples from 297 individuals at risk for HBV in local clinical settings (health fairs and outreach events) in parallel with commercial laboratory HBsAg testing (Quest Diagnostics EIA). POC testing was 73.7% sensitive and 97.8% specific for detection of HBsAg. Although the POC test demonstrated high sensitivity over a range of genotypes, false negatives were frequent in a clinical setting. Nevertheless, the POC assay offers advantages for testing in both developed and resource‐limited countries due to its low cost (0.50$) and immediately available results.
Occurrence of Metabolic Osteopathy in Patients with Chronic Pancreatitis

Introduction: Chronic pancreatitis is an inflammatory disease manifested by maldigestion and, in an advanced stage, by malabsorption. The aim of our research was to monitor the occurrence of metabolic osteopathies (osteopenia, osteoporosis and osteomalacia) in patients with chronic pancreatitis. Patients and Methods: The group consisted of 73 patients (17 women and 56 men) in different stages of chronic pancreatitis. In all patients we determined serum concentrations of Ca, P, 25-OH vitamin D, 1,25-(OH)2 vitamin D, alkaline phosphatase and its bone isoenzyme. Bone mineral density was measured by dual-energy X-ray absorptiometry (DXA) in the lumbar spine (L1–L4) and in the proximal femur. When bone pathology was identified by DXA, we determined the other to exclude other causes of secondary osteopathy and the 24-hour loss of calcium and phosphorus in the urine. Results: Osteopathy was found in 39% of patients, i.e. osteopenia in 26%, osteoporosis in 5% and osteomalacia in 8% of cases. Conclusion: The occurrence of relatively high percentages of metabolic osteopathies in patients with chronic pancreatitis may correlate, namely in advanced stages of the disease, with the malabsorption of vitamin D to the enterohepatic circulation. In initial forms of pancreatitis, it is not possible to exclude progression of osteopathy due to changes of the intestinal flora, with disturbance of vitamin D absorption to the intestinal mucosa.
Gaussian Process Latent Variable Models for Visualisation of High Dimensional Data

In this paper we introduce a new underlying probabilistic model for principal component analysis (PCA). Our formulation interprets PCA as a particular Gaussian process prior on a mapping from a latent space to the observed data-space. We show that if the prior's covariance function constrains the mappings to be linear the model is equivalent to PCA, we then extend the model by considering less restrictive covariance functions which allow non-linear mappings. This more general Gaussian process latent variable model (GPLVM) is then evaluated as an approach to the visualisation of high dimensional data for three different data-sets. Additionally our non-linear algorithm can be further kernelised leading to 'twin kernel PCA' in which a mapping between feature spaces occurs.
Understanding the Mechanism of Atovaquone Drug Resistance in Plasmodium falciparum Cytochrome b Mutation Y268S Using Computational Methods

The rapid appearance of resistant malarial parasites after introduction of atovaquone (ATQ) drug has prompted the search for new drugs as even single point mutations in the active site of Cytochrome b protein can rapidly render ATQ ineffective. The presence of Y268 mutations in the Cytochrome b (Cyt b) protein is previously suggested to be responsible for the ATQ resistance in Plasmodium falciparum (P. falciparum). In this study, we examined the resistance mechanism against ATQ in P. falciparum through computational methods. Here, we reported a reliable protein model of Cyt bc1 complex containing Cyt b and the Iron-Sulphur Protein (ISP) of P. falciparum using composite modeling method by combining threading, ab initio modeling and atomic-level structure refinement approaches. The molecular dynamics simulations suggest that Y268S mutation causes ATQ resistance by reducing hydrophobic interactions between Cyt bc1 protein complex and ATQ. Moreover, the important histidine contact of ATQ with the ISP chain is also lost due to Y268S mutation. We noticed the induced mutation alters the arrangement of active site residues in a fashion that enforces ATQ to find its new stable binding site far away from the wild-type binding pocket. The MM-PBSA calculations also shows that the binding affinity of ATQ with Cyt bc1 complex is enough to hold it at this new site that ultimately leads to the ATQ resistance.
Assessing the effect of dynamics on the closed-loop protein-folding hypothesis

The closed-loop (loop-n-lock) hypothesis of protein folding suggests that loops of about 25 residues, closed through interactions between the loop ends (locks), play an important role in protein structure. Coarse-grain elastic network simulations, and examination of loop lengths in a diverse set of proteins, each supports a bias towards loops of close to 25 residues in length between residues of high stability. Previous studies have established a correlation between total contact distance (TCD), a metric of sequence distances between contacting residues (cf. contact order), and the log-folding rate of a protein. In a set of 43 proteins, we identify an improved correlation (r2 = 0.76), when the metric is restricted to residues contacting the locks, compared to the equivalent result when all residues are considered (r2 = 0.65). This provides qualified support for the hypothesis, albeit with an increased emphasis upon the importance of a much larger set of residues surrounding the locks. Evidence of a similar-sized protein core/extended nucleus (with significant overlap) was obtained from TCD calculations in which residues were successively eliminated according to their hydrophobicity and connectivity, and from molecular dynamics simulations. Our results suggest that while folding is determined by a subset of residues that can be predicted by application of the closed-loop hypothesis, the original hypothesis is too simplistic; efficient protein folding is dependent on a considerably larger subset of residues than those involved in lock formation.
Cognitive therapy versus fluoxetine in generalized social phobia: a randomized placebo-controlled trial.

Sixty patients meeting Diagnostic and Statistical Manual of Mental Disorders (4th ed.: American Psychiatric Association, 1994) criteria for generalized social phobia were assigned to cognitive therapy (CT), fluoxetine plus self-exposure (FLU + SE), or placebo plus self-exposure (PLA + SE). At posttreatment (16 weeks), the medication blind was broken. CT and FLU + SE patients then entered a 3-month booster phase. Assessments were at pretreatment, midtreatment, posttreatment, end of booster phase, and 12-month follow-up. Significant improvements were observed on most measures in all 3 treatments. On measures of social phobia, CT was superior to FLU + SE and PLA + SE at midtreatment and at posttreatment. FLU + SE and PLA + SE did not differ. CT remained superior to FLU + SE at the end of the booster period and at 12-month follow-up. On general mood measures, there were few differences between the treatments
Do Actions Speak Louder than Words? The Response of Asset Prices to Monetary Policy Actions and Statements

We investigate the effects of U.S. monetary policy on asset prices using a high-frequency event-study analysis. We test whether these effects are adequately captured by a single factor-changes in the federal funds rate target - and find that they are not. Instead, we find that two factors are required. These factors have a structural interpretation as a "current federal funds rate target" factor and a "future path of policy" factor, with the latter closely associated with Federal Open Market Committee statements.We measure the effects of these two factors on bond yields and stock prices using a new intraday data set going back to 1990. According to our estimates, both monetary policy actions and statements have important but differing effects on asset prices, with statements having a much greater impact on longer-term Treasury yields.
Surface markers on leukemia and lymphoma cells: recent advances.

Recent advances in immunology have led to important insights into leukocyte differentiation and the cellular ongin of leukemia. It is now possible to precisely define stages of human lymphocyte and gnanulocyte differentiation utilizing highly specific monoclonal antibodies that define cell surface antigens in conjunction with more traditional markers such as surface and cytoplasmic immunoglobulin on B lymphocytes, sheep erythnocyte (E) receptors on T lymphocytes, and cytochemical staining of myeloid cells. Five major subtypes of acute lymphoblastic leukemia (ALL) are now recognized, including unclassified or null ALL, common ALL (cALL), pre-B-ALL, B-ALL, and T-ALL. Within the T-ALL subgroup. there is considerable heterogeneity based on the presence or absence of the E-receptor and various T-cell surface membrane antigens defined by monoclonal antibodies. Cells from patients with chronic lym-
Comparison of neural activity preceding reaches to auditory and visual stimuli in the parietal reach region

We examined the responses of neurons in the parietal reach region (PRR) during reaches to the remembered locations of auditory or visual stimuli. We found that the firing rate of PRR neurons contained information about the location of auditory and visual stimuli. For neurons tested with visual stimuli, the amount of information remained constant throughout the task. In contrast, for neurons tested with auditory stimuli, the amount of target-location information increased as the trial evolved. During the reach period of the task, the amount of information that was carried by neurons tested with auditory stimuli was not statistically different from the amount carried by neurons tested with visual stimuli. We interpret these data to suggest that the type of information that PRR neurons encode evolves throughout a task.
Assessment of the Atka mackerel stock in the Bering Sea and Aleutian Islands

1. The 2017 catch estimate was updated, and estimated total catch for 2018 was set equal to the TAC (71,000 t). 2. Estimated 2019 and 2020 catches are 58,900 t and 54,500 t, respectively. 3. The 2017 fishery age composition data were added. 4. The 2018 Aleutian Islands survey biomass estimates were added. 5. The estimated average selectivity for 2013-2017 was used for projections. 6. We assume that approximately 86% of the BSAI-wide ABC is likely to be taken under the revised Steller Sea Lion Reasonable and Prudent Alternatives (SSL RPAs) implemented in 2015. This percentage was applied to the 2019 and 2020 maximum permissible ABCs, and those reduced amounts were assumed to be caught in order to estimate the 2019 and 2020 ABCs and OFL values. 7. As in 2017, the sample sizes specified for fishery age composition data were rescaled to have the same means as in the original baseline model (100), but varied relative to the number of hauls for the fishery. The 2017 data were added. 8. The 1986 survey age data were removed.
The Role of Chlamydia pneumoniae in the Atherosclerotic Process of Patients under 50 Years of Age Who Underwent Coronary Artery Bypass Graft Surgery

Background: To evaluate the presence of C. pneumoniae DNA in the tissues and C. pneumoniae DNA antibodies in the blood samples of patients who underwent CABG surgery. Material and Methods: Fifty-one patients aorta. C. pneumoniae DNA was evaluated in the tissues collected from the atrium, left internal thoracic artery and ascending aorta of patients. Results: Although, C. pneumoniae DNA was negative in the atrial and left internal thoracic artery tissues of all patients, it was positive in the tissues obtained from the ascending aortas of twelve patients. C. pneumoniae DNA positivity was significantly higher in patients with increased aortic intimal thickness compared to those without increased aortic thickness. Conclusion: The question whether C. pneumoniae is triggering atherosclerosis or is involved as a super-infection could not be clarified.
Panning for Long Noncoding RNAs

The recent advent of high-throughput approaches has revealed widespread transcription of the human genome, leading to a new appreciation of transcription regulation, especially from noncoding regions. Distinct from most coding and small noncoding RNAs, long noncoding RNAs (lncRNAs) are generally expressed at low levels, are less conserved and lack protein-coding capacity. These intrinsic features of lncRNAs have not only hampered their full annotation in the past several years, but have also generated controversy concerning whether many or most of these lncRNAs are simply the result of transcriptional noise. Here, we assess these intrinsic features that have challenged lncRNA discovery and further summarize recent progress in lncRNA discovery with integrated methodologies, from which new lessons and insights can be derived to achieve better characterization of lncRNA expression regulation. Full annotation of lncRNA repertoires and the implications of such annotation will provide a fundamental basis for comprehensive understanding of pervasive functions of lncRNAs in biological regulation.
Hybrid Thermostatic Approximations of Junctions for Some Optimal Control Problems on Networks

The aim of this paper is to study some optimal control problems on networks with junctions. We consider an approximation of such a problems given by the use of a switching rule of delay-relay type and study the passage to the limit when $\varepsilon$, the parameter of the approximation, goes to zero. First, we take into account a twofold junction problem for which we characterize the limit function as viscosity solution and maximal subsolution of a suitable Hamilton-Jacobi problem. Afterwards we analyse a threefold junction problem for which we consider two different way for passing to the limit in its approximation. For both ways we recover some uniqueness results in the sense of maximal subsolution.
Sources of uncertainty in estuarine climate impact modeling

Early planning decisions which take into account the impact of climate change have to be made under uncertainty. Thus, the explicit investigation of the level of uncertainty in climate impact research is becoming increasingly important. This article focusses on uncertainties in a climate impact assessment for the Weser estuary, Germany. The basis is a mean sea level rise scenario which is studied with a 3D baroclinic impact model. Uncertainties due to model parameters, structural limitations of the model, boundary conditions, the scenario uncertainty and variability in the impact model are discussed. The uncertainties due to natural variability and roughness are investigated by means of changes in high and low water levels. The results show that the uncertainty related to the impact model and the chosen model parameters in this study is small compared to the uncertainty induced by the natural variability and the boundary conditions.
Multidecadal Changes and Interannual Variation in Springtime Phenology of North American Temperate and Boreal Deciduous Forests

The timing of leaf emergence is an important diagnostic of climate change impacts on ecosystems. Here we present the first continental‐scale analysis of multidecadal changes in the timing of spring onset across North American temperate and boreal forests based on Landsat imagery. Our results show that leaf emergence in Eastern Temperate Forests has consistently trended earlier, with a median change of about 1 week over the 30 year study period. Changes in leaf emergence dates in boreal forests were more heterogeneous, with some sites showing trends toward later dates. Interannual variability in leaf emergence dates was strongly sensitive to springtime accumulated growing degree days across all sites, and geographic patterns of changes in onset dates were highly correlated with changes in regional springtime temperatures. These results provide a refined characterization of recent changes in springtime forest phenology and improve understanding regarding the sensitivity of North American forests to climate change.
Transition paths, diffusive processes, and preequilibria of protein folding

Fundamental relationships between the thermodynamics and kinetics of protein folding were investigated using chain models of natural proteins with diverse folding rates by extensive comparisons between the distribution of conformations in thermodynamic equilibrium and the distribution of conformations sampled along folding trajectories. Consistent with theory and single-molecule experiment, duration of the folding transition paths exhibits only a weak correlation with overall folding time. Conformational distributions of folding trajectories near the overall thermodynamic folding/unfolding barrier show significant deviations from preequilibrium. These deviations, the distribution of transition path times, and the variation of mean transition path time for different proteins can all be rationalized by a diffusive process that we modeled using simple Monte Carlo algorithms with an effective coordinate-independent diffusion coefficient. Conformations in the initial stages of transition paths tend to form more nonlocal contacts than typical conformations with the same number of native contacts. This statistical bias, which is indicative of preferred folding pathways, should be amenable to future single-molecule measurements. We found that the preexponential factor defined in the transition state theory of folding varies from protein to protein and that this variation can be rationalized by our Monte Carlo diffusion model. Thus, protein folding physics is different in certain fundamental respects from the physics envisioned by a simple transition-state picture. Nonetheless, transition state theory can be a useful approximate predictor of cooperative folding speed, because the height of the overall folding barrier is apparently a proxy for related rate-determining physical properties.
Involvement of O-glycosylation defining oncofetal fibronectin in epithelial-mesenchymal transition process

The process termed “epithelial–mesenchymal transition” (EMT) was originally discovered in ontogenic development, and has been shown to be one of the key steps in tumor cell progression and metastasis. Recently, we showed that the expression of some glycosphingolipids (GSLs) is down-regulated during EMT in human and mouse cell lines. Here, we demonstrate the involvement of GalNAc-type (or mucin-type) O-glycosylation in EMT process, induced with transforming growth factor β (TGF-β) in human prostate epithelial cell lines. We found that: (i) TGF-β treatment caused up-regulation of oncofetal fibronectin (onfFN), which is defined by mAb FDC6, and expressed in cancer or fetal cells/tissues, but not in normal adult cells/tissues. The reactivity of mAb FDC6 requires the addition of an O-glycan at a specific threonine, inside the type III homology connective segment (IIICS) domain of FN. (ii) This change is associated with typical EMT characteristics; i.e., change from epithelial to fibroblastic morphology, enhanced cell motility, decreased expression of a typical epithelial cell marker, E-cadherin, and enhanced expression of mesenchymal markers. (iii) TGF-β treatment up-regulated mRNA level of FN containing the IIICS domain and GalNAc-T activity for the IIICS domain peptide substrate containing the FDC6 onfFN epitope. (iv) Knockdown of GalNAc-T6 and T3 inhibited TGF-β–induced up-regulation of onfFN and EMT process. (v) Involvement of GSLs was not detectable with the EMT process in these cell lines. These findings indicate the important functional role of expression of onfFN, defined by site-specific O-glycosylation at IIICS domain, in the EMT process.