Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of the Specificities of IgG, IgG-Subclass, IgA and IgM Reactivities in African and European HIV-Infected Individuals with an HIV-1 Clade C Proteome-Based Array

A comprehensive set of recombinant proteins and peptides of the proteome of HIV-1 clade C was prepared and purified and used to measure IgG, IgG-subclass, IgA and IgM responses in HIV-infected patients from Sub-Saharan Africa, where clade C is predominant. As a comparison group, HIV-infected patients from Europe were tested. African and European patients showed an almost identical antibody reactivity profile in terms of epitope specificity and involvement of IgG, IgG subclass, IgA and IgM responses. A V3-peptide of gp120 was identified as major epitope recognized by IgG1>IgG2 = IgG4>IgG3, IgA>IgM antibodies and a C-terminal peptide represented another major peptide epitope for the four IgG subclasses. By contrast, gp41-derived-peptides were mainly recognized by IgG1 but not by the other IgG subclasses, IgA or IgM. Among the non-surface proteins, protease, reverse transcriptase+RNAseH, integrase, as well as the capsid and matrix proteins were the most frequently and strongly recognized antigens which showed broad IgG subclass and IgA reactivity. Specificities and magnitudes of antibody responses in African patients were stable during disease and antiretroviral treatment, and persisted despite severe T cell loss. Using a comprehensive panel of gp120, gp41 peptides and recombinant non-surface proteins of HIV-1 clade C we found an almost identical antibody recognition profile in African and European patients regarding epitopes and involved IgG-sublass, IgA- and IgM-responses. Immune recognition of gp120 peptides and non-surface proteins involved all four IgG subclasses and was indicative of a mixed Th1/Th2 immune response. The HIV-1 clade C proteome-based test allowed diagnosis and monitoring of antibody responses in the course of HIV-infections and assessment of isotype and subclass responses.
Application of different markers and data-analysis tools to the examination of biodiversity can lead to different results: a case study with Starmerella bacillaris (synonym Candida zemplinina) strains

Starmerella bacillaris (Candida zemplinina) is a genetically heterogeneous species. In this work, the diversity of 41 strains of various origins is examined and compared by the analysis of the length polymorphism of nuclear microsatellites and the RFLP of mitochondrial genomes. The band patterns are analysed with UPGMA, neighbor joining, neighbor net, minimum spanning tree and non-metric MDS algorithms. The results and their comparison to previous analyses demonstrate that different markers and different clustering methods can result in very different groupings of the same strains. The observed differences between the topologies of the dendrograms also indicate that the positions of the strains do not necessarily reflect their real genetic relationships and origins. The possibilities that the differences might be partially due to different sensitivity of the markers to environmental factors (selection pressure) and partially to the different grouping criteria of the algorithms are also discussed.
Duration-controllable square-wave pulse from an L band dissipative soliton fiber laser based on the dispersive Fourier transformation technique

We experimentally generated the duration-controllable square-wave pulse from an L band dissipative soliton (DS) fiber laser based on the dispersive Fourier transformation (DFT) technique. The rectangular spectrum emitted from an L band dissipative soliton fiber laser is mapped into a time-domain coherent rectangular waveform through the DFT technique. The duration of the square-wave pulse can be controllable with the adjustments of the pump power. The results demonstrate that it is an effective and flexible way to achieve duration-controllable square-wave pulses by combinating with DFT technique and DS fiber laser.
DEC-A*: A Decentralized A* Algorithm

A* is the algorithm of finding the shortest path between two nodes in a graph. When the searching problem is constituted of a set of linked graphs, A* searches solution like if it is face of one graph formed by linked graphs. While researchers have developed solutions to reduce the execution time of A* in multiple cases by multiples techniques, we develop a new algorithm: DEC-A* which is a decentralized version of A* composing a solution through a collection of graph. A* uses a distance-plus-cost heuristic function to determine the order in which the search visits nodes in the tree. Our algorithm DEC-A* extends the evaluation of the distanceplus-cost heuristic to be the sum of two functions : local distance, which evaluates the cost to reach the nearest neighbor node s to the goal, and global distance which evaluates the cost from s to the goal through other graphs. DEC-A* reduces the time of finding the shortest path and reduces the complexity, while ensuring the privacy of graphs.
Second-Line Antiretroviral Therapy in Sub-Saharan Africa: It Is Time to Mind the Gaps

Abstract The delay between first-line antiretroviral therapy (ART) failure and initiation of second-line ART in resource-limited settings can be prolonged. Increasing evidence links delayed antiretroviral switch with increased risk for opportunistic infection (OI) and death, particularly in patients with advanced HIV at the time of first-line failure. As access to viral load (VL) monitoring widens beyond a few countries, mechanisms are needed to optimize the use of routine virologic monitoring and assure that first-line regimen failure results in prompt second-line switch. For patients with advanced HIV or OI at the time of first-line failure, a targeted fast track to second-line ART should be considered, involving a switch to second-line ART during a single visit. To derive the maximum benefit from both the current expansion of VL monitoring and the falling costs of second-line ART, clinics and healthcare workers should be given the tools and training to detect and switch patients with regimen failure before HIV disease progression.
Genetic Evidence Highlights Potential Impacts of By-Catch to Cetaceans

Incidental entanglement in fishing gear is arguably the most serious threat to many populations of small cetaceans, judging by the alarming number of captured animals. However, other aspects of this threat, such as the potential capture of mother-offspring pairs or reproductive pairs, could be equally or even more significant but have rarely been evaluated. Using a combination of demographic and genetic data we provide evidence that i) Franciscana dolphin pairs that are potentially reproductive and mother-offspring pairs form temporal bonds, and ii) are entangled simultaneously. Our results highlight potential demographic and genetic impacts of by-catch to cetacean populations: the joint entanglement of mother-offspring or reproductive pairs, compared to random individuals, might exacerbate the demographic consequences of by-catch, and the loss of groups of relatives means that significant components of genetic diversity could be lost together. Given the social nature of many odontocetes (toothed cetaceans), we suggest that these potential impacts could be rather general to the group and therefore by-catch could be more detrimental than previously considered.
A new study on mammographic image denoising using multiresolution techniques

Mammography is the most simple and effective technology for early detection of breast cancer. However, the lesion areas of breast are difficult to detect which due to mammograms are mixed with noise. This work focuses on discussing various multiresolution denoising techniques which include the classical methods based on wavelet and contourlet; moreover the emerging multiresolution methods are also researched. In this work, a new denoising method based on dual tree contourlet transform (DCT) is proposed, the DCT possess the advantage of approximate shift invariant, directionality and anisotropy. The proposed denoising method is implemented on the mammogram, the experimental results show that the emerging multiresolution method succeeded in maintaining the edges and texture details; and it can obtain better performance than the other methods both on visual effects and in terms of the Mean Square Error (MSE), Peak Signal to Noise Ratio (PSNR) and Structure Similarity (SSIM) values.
Simulation and analysis of mold filling in water-assisted injection molding of viscoelastic polymers

At present, water-assisted injection molding is suitable for producing hollow or part of hollow plastic products. The research of viscoelastic properties can provide an improved understanding about the influence of related process parameters on the filling process of water-assisted injection molded parts. In this paper, based on the open source code of OpenFOAM, an analysis module was constructed for the three dimensional isothermal flow of multiphase fluid which can be subscribed as Giesekus viscoelastic model, by the object oriented program and the volume of fluid method(VOF). The filling process of the water-assisted injection molding was simulated by the solver called viscoelastic InterFoam. The result agrees with the experiment of Polynkin, which shows that with increase of the injection rate, the residual wall thickness of melt and penetration distance of water will be increased. That can be analyzed according to viscoelastic properties of melt.
System of aided classification of ground objects by video observation from unmanned aerial vehicle

Analysis of classification system by video observation has been done. The system with aided classification based on probabilistic models is proposed. Feature vector contains the most informative components and allows the minimization of decision risks. Results have proven the reliability of classification during a number of video frames in the condition of non-full data descriptive space.
Serial Plasma Metabolites Following Hypoxic-Ischemic Encephalopathy in a Nonhuman Primate Model

Biomarkers that indicate the severity of hypoxic-ischemic brain injury and response to treatment and that predict neurodevelopmental outcomes are urgently needed to improve the care of affected neonates. We hypothesize that sequentially obtained plasma metabolomes will provide indicators of brain injury and repair, allowing for the prediction of neurodevelopmental outcomes. A total of 33 Macaca nemestrina underwent 0, 15 or 18 min of in utero umbilical cord occlusion (UCO) to induce hypoxic-ischemic encephalopathy and were then delivered by hysterotomy, resuscitated and stabilized. Serial blood samples were obtained at baseline (cord blood) and at 0.1, 24, 48, and 72 h of age. Treatment groups included nonasphyxiated controls (n = 7), untreated UCO (n = 11), UCO + hypothermia (HT; n = 6), and UCO + HT + erythropoietin (n = 9). Metabolites were extracted and analyzed using comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry and quantified by PARAFAC (parallel factor analysis). Using nontargeted discovery-based methods, we identified 63 metabolites as potential biomarkers. The changes in metabolite concentrations were characterized and compared between treatment groups. Further comparison determined that 8 metabolites (arachidonic acid, butanoic acid, citric acid, fumaric acid, lactate, malate, propanoic acid, and succinic acid) correlated with early and/or long-term neurodevelopmental outcomes. The combined outcomes of death or cerebral palsy correlated with citric acid, fumaric acid, lactate, and propanoic acid. This change in circulating metabolome after UCO may reflect cellular metabolism and biochemical changes in response to the severity of brain injury and have potential to predict neurodevelopmental outcomes.
Too Long, Too Short, or Too Variable? Sleep Intraindividual Variability and Its Associations With Perceived Sleep Quality and Mood in Adolescents During Naturalistically Unconstrained Sleep

Introduction: Research has extensively examined the relationship between adolescents' mental health and average sleep duration/quality. Using rigorous methodology, this study characterized adolescents' objective sleep intraindividual variability (IIV) and examined its role on mood beyond the effects of their respective individual mean (IIM) values. Aims and Methods: One hundred forty‐six community‐dwelling adolescents (47.3% male) aged 16.2 ± 1.0 (M ± SD) years wore an actigraph that assessed bedtime, risetime, time‐in‐bed (TIB), and sleep onset latency (SOL) throughout a 15‐day vacation with relatively unconstrained sleep opportunity. Self‐report sleep quality (SSQ), negative mood (MOOD), and other covariates were assessed using questionnaires. For each sleep variable, individuals' mean values (IIM) and IIV were used to simultaneously predict MOOD with SSQ as a mediator. Models were estimated in a Bayesian IIV framework; both linear and quadratic effects of the IIM and IIV were examined. Results: Longer and more variable TIB, as well as more variable SOL (but not mean SOL), were associated with poorer SSQ (ps < .01), which in turn, was associated with more negative MOOD (ps < .05). The indirect effect of SOL IIV was curvilinear, such that as SOL became more variable, the deteriorating effect of high SOL IIV accelerated. Neither bedtime nor risetime IIV was significantly associated with SSQ or MOOD. Conclusions: During relatively unconstrained sleep opportunity, more variable TIB and SOL were associated with more negative mood, mediated by poorer perceived sleep quality. Significant effects of IIV were over and above that of mean values, suggesting that unique aspects of sleep IIV are relevant to how adolescents perceive sleep quality and their mood.
Iron deficiency protects against severe Plasmodium falciparum malaria and death in young children.

BACKGROUND Iron supplementation may increase malaria morbidity and mortality, but the effect of naturally occurring variation in iron status on malaria risk is not well studied. METHODS A total of 785 Tanzanian children living in an area of intense malaria transmission were enrolled at birth, and intensively monitored for parasitemia and illness including malaria for up to 3 years, with an average of 47 blood smears. We assayed plasma samples collected at routine healthy-child visits, and evaluated the impact of iron deficiency (ID) on future malaria outcomes and mortality. RESULTS ID at routine, well-child visits significantly decreased the odds of subsequent parasitemia (23% decrease, P < .001) and subsequent severe malaria (38% decrease, P = .04). ID was also associated with 60% lower all-cause mortality (P = .04) and 66% lower malaria-associated mortality (P = .11). When sick visits as well as routine healthy-child visits are included in analyses (average of 3 iron status assays/child), ID reduced the prevalence of parasitemia (6.6-fold), hyperparasitemia (24.0-fold), and severe malaria (4.0-fold) at the time of sample collection (all P < .001). CONCLUSIONS Malaria risk is influenced by physiologic iron status, and therefore iron supplementation may have adverse effects even among children with ID. Future interventional studies should assess whether treatment for ID coupled with effective malaria control can mitigate the risks of iron supplementation for children in areas of malaria transmission.
Identifying seedling root architectural traits associated with yield and yield components in wheat

Background and Aims Plant roots growing underground are critical for soil resource acquisition, anchorage and plant-environment interactions. In wheat ( Triticum aestivum ), however, the target root traits to improve yield potential still remain largely unknown. This study aimed to identify traits of seedling root system architecture (RSA) associated with yield and yield components in 226 recombinant inbred lines (RILs) derived from a cross between the bread wheat Triticum aestivum 'Forno' (small, wide root system) and spelt Triticum spelta 'Oberkulmer' (large, narrow root system). Methods A 'pouch and wick' high-throughput phenotyping pipeline was used to determine the RSA traits of 13-day-old RIL seedlings. Two field experiments and one glasshouse experiment were carried out to investigate the yield, yield components and phenology, followed by identification of quantitative trait loci (QTLs). Key Results There was substantial variation in RSA traits between genotypes. Seminal root number and total root length were both positively associated with grains m -2 , grains per spike, above-ground biomass m -2 and grain yield. More seminal roots and longer total root length were also associated with delayed maturity and extended grain filling, likely to be a consequence of more grains being defined before anthesis. Additionally, the maximum width of the root system displayed positive relationships with spikes m -2 , grains m -2 and grain yield. Ten RILs selected for the longest total roots exhibited the same effects on yield and phenology as described above, compared with the ten lines with the shortest total roots. Genetic analysis revealed 38 QTLs for the RSA, and QTL coincidence between the root and yield traits was frequently observed, indicating tightly linked genes or pleiotropy, which concurs with the results of phenotypic correlation analysis. Conclusions Based on the results from the Forno × Oberkulmer population, it is proposed that vigorous early root growth, particularly more seminal roots and longer total root length, is important to improve yield potential, and should be incorporated into wheat ideotypes in breeding.
Closed-loop Neuropharmacology for Epilepsy: Distant Dream or Future Reality?

Abstract: Epilepsy is considered the most frequent severe neurological condition but most patients treated with medication become seizure free. The management of treatment, however, is highly empirical, mainly relying on observation. A closed-loop therapy for epilepsy would be very valuable for more efficient treatment regimens. Here we discuss monitoring treat-ment (therapeutic drug monitoring) and the potential developments in this field, as well as providing a review of potential bi-omarkers that could be used to monitor the disease activity. Finally, we consider the pharmacogenetic input in epilepsy treat-ment
Automatic verification for deadlock in networks-on-chips with adaptive routing and wormhole switching

Wormhole switching is a switching technique nowadays commonly used in networks-on-chips (NoCs). It is efficient but prone to deadlock. The design of a deadlock-free adaptive routing function constitutes an important challenge. We present a novel algorithm for the automatic verification that a routing function is deadlock-free in wormhole networks. A sufficient condition for deadlock-free routing and an associated algorithm are defined. The algorithm is proven complete for the condition. The condition, the algorithm, and the correctness theorem have been formalized and checked in the logic of the ACL2 interactive theorem proving system. The algorithm has a time complexity in O(N3), where N denotes the number of nodes in the network. This outperforms the previous solution of Taktak et al. by one degree. Experimental results confirm the high efficiency of our algorithm. This paper presents a formally proven correct algorithm that detects deadlocks in a 2D-mesh with about 4000 nodes and 15000 channels within seconds.
Multi-Device Fusion for Enhanced Contextual Awareness of Localization in Indoor Environments

Recently, with various developing sensors, mobile devices have become interesting in the research community for indoor localization. In this paper, we propose Twi-Adaboost, a collaborative indoor localization algorithm with the fusion of internal sensors, such as the accelerometer, gyroscope, and magnetometer from multiple devices. Specifically, the data sets are collected first by one person wearing two devices simultaneously: a smartphone and a smartwatch, each collecting multivariate data represented by their internal parameters in a real environment. Then, we evaluate the data sets from these two devices for their strengths and weaknesses in recognizing the indoor position. Based on that, the Twi-AdaBoost algorithm, an interactive ensemble learning method, is proposed to improve the indoor localization accuracy by fusing the co-occurrence information. The performance of the proposed algorithm is assessed on a real-world dataset. The experiment results demonstrate that Twi-AdaBoost achieves a localization error about 0.39 m on average with a low deployment cost, which outperforms the state-of-the-art indoor localization algorithms.
Inhibition of lung cancer cells A549 and H460 by curcuminoid extracts and nanoemulsions prepared from Curcuma longa Linnaeus

The objectives of this study were to explore the inhibition mechanism of lung cancer cells A549 and H460 by curcuminoid extracts and nanoemulsions prepared from Curcuma longa Linnaeus. In addition, human bronchus epithelial cell line BEAS-2B (normal cell) was selected for comparison. A high-performance liquid chromatography (HPLC) method was developed to separate and quantify the various curcuminoids in C. longa extract, including curcumin (1,714.5 μg/mL), demethoxycurcumin (1,147.4 μg/mL), and bisdemethoxycurcumin (190.2 μg/mL). A high-stability nanoemulsion composed of Tween 80, water, and curcuminoid extract was prepared, with mean particle size being 12.6 nm. The cell cycle was retarded at G2/M for both the curcuminoid extract and nanoemulsion treatments; however, the inhibition pathway may be different. H460 cells were more susceptible to apoptosis than A549 cells for both curcuminoid extract and nanoemulsion treatments. Growth of BEAS-2B remained unaffected for both the curcuminoid extract and nanoemulsion treatments, with a concentration range from 1 to 4 μg/mL. Also, the activities of caspase-3, caspase-8, and caspase-9 followed a dose-dependent increase for both A549 and H460 cells for both the treatments, accompanied by a dose-dependent increase in cytochrome C expression and a dose-dependent decrease in CDK1 expression. Interestingly, a dose-dependent increase in cyclin B expression was shown for A549 cells for both the treatments, while a reversed trend was found for H460 cells. Both mitochondria and death receptor pathways may be responsible for apoptosis of both A549 and H460 cells.
Impact of body mass index on outcomes following mitral surgery: does an obesity paradox exist?

OBJECTIVES This study was conducted to clarify the relationship between body mass index and mitral valve (MV) surgery and to determine whether an 'obesity paradox' exists in the context of surgery for degenerative MV disease. METHODS In this retrospective single-centre study, we analysed data from 715 patients who underwent mitral surgery for degenerative disease from 2000 to 2015. Patients were classified according to body mass index: underweight (<20 kg/m2), normal weight (20-24.99 kg/m2), overweight (25-29.99 kg/m2) and obese (≥30 kg/m2). Early and long-term results were investigated. Multivariable analysis was conducted to identify risk factors for long-term mortality. RESULTS Mean follow-up was 67 ± 44 months (range 0-190 months). There were no differences between groups regarding 30-day mortality (P = 0.35), stroke (P = 0.45), reoperation for bleeding (P = 0.9) and length of hospital stay (P = 0.31). Obese patients were at increased risk of acute kidney injury when compared with normal weight patients (17% vs 5%; P = 0.03) but not when compared with the other groups; this was confirmed within the subgroup with depressed ejection fraction (42% vs 10%, P = 0.02). No differences in long-term survival were found across groups for all patients (P = 0.62) and for patients with depressed ejection fraction (P = 0.6), with a trend towards worse survival in obese patients undergoing MV repair (P = 0.06). Survival in obese patients undergoing repair was significantly worse than that in obese patients undergoing replacement (P = 0.04). CONCLUSIONS An 'obesity paradox' was not demonstrated after surgery for degenerative MV disease. Obese patients are more prone to acute kidney injury and have worse late survival after MV repair.