Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a peptide blocking vascular endothelial growth factor (VEGF)‐mediated angiogenesis

Vascular endothelial growth factor (VEGF) binding to the kinase domain receptor (KDR/FLK1 or VEGFR‐2) mediates vascularization and tumor‐induced angiogenesis. Since there is evidence that KDR plays an important role in tumor angiogenesis, we sought to identify peptides able to block the VEGF–KDR interaction. A phage epitope library was screened by affinity for membrane‐expressed KDR or for an anti‐VEGF neutralizing monoclonal antibody. Both strategies led to the isolation of peptides binding KDR specifically, but those isolated by KDR binding tended to display lower reactivities. Of the synthetic peptides corresponding to selected clones tested to determine their inhibitory activity, ATWLPPR completely abolished VEGF binding to cell‐displayed KDR. In vitro, this effect led to the inhibition of the VEGF‐mediated proliferation of human vascular endothelial cells, in a dose‐dependent and endothelial cell type‐specific manner. Moreover, in vivo, ATWLPPR totally abolished VEGF‐induced angiogenesis in a rabbit corneal model. Taken together, these data demonstrate that ATWLPPR is an effective antagonist of VEGF binding, and suggest that this peptide may be a potent inhibitor of tumor angiogenesis and metastasis.
Infectious Bronchitis Viruses with a Novel Genomic Organization

ABSTRACT A number of novel infectious bronchitis viruses (IBVs) were previously identified in commercial poultry in Australia, where they caused significant economic losses. Since there has been only limited characterization of these viruses, we investigated the genomic and phenotypic differences between these novel IBVs and other, classical IBVs. The 3′ 7.5 kb of the genomes of 17 Australian IBV strains were sequenced, and growth properties of 6 of the strains were compared. Comparison of sequences of the genes coding for structural and nonstructural proteins revealed the existence of two IBV genotypes: classical and novel. The genomic organization of the classical IBVs was typical of those of other group III coronaviruses: 5′-Pol-S-3a-3b-E-M-5a-5b-N-untranslated region (UTR)-3′. However, the novel IBV genotype lacked either all or most of the genes coding for nonstructural proteins at the 3′ end of the genome and had a unique open reading frame, X1. The gene order was either 5′-Pol-S-X1-E-M-N-UTR-3′ or 5′-Pol-S-X1-E-M-5b-N-UTR-3′. Phenotypically, novel and classical IBVs also differed; novel IBVs grew at a slower rate and reached lower titers in vitro and in vivo and were markedly less immunogenic in chicks. Although the novel IBVs induced histopathological lesions in the tracheas of infected chicks that were comparable to those induced by classical strains, they did not induce lesions in the kidneys. This study has demonstrated for the first time the existence of a naturally occurring IBV genotype devoid of some of the genes coding for nonstructural proteins and has also indicated that all of the accessory genes are dispensable for the growth of IBV and that such viruses are able to cause clinical disease and economic loss. The phylogenic differences between these novel IBVs and other avian coronaviruses suggest a reservoir host distinct from domestic poultry.
Planar transformers with no common mode noise generation for flyback and forward converters

Flyback and Forward converters are two commonly used topologies for isolated low power applications. In order to enhance the performance of these converters, planar transformers (PT) can be used that feature lower height, considerably lower leakage inductance, excellent thermal characteristics, repeatability, and manufacturing simplicity. Selecting a proper winding arrangement for PT is a significant challenge, in particular given the large capacitances involved in flat structures. While interleaved structures significantly reduce the AC resistance and leakage inductance of PTs, they also lead to very large inter-winding capacitance, which produces significant levels of undesired common-mode (CM) noise that causes EMI problems. This paper focuses on the creation of interleaved winding structures that minimize CM noise and EMI commonly present in PT and at the same time achieves low AC resistance and leakage inductance. The experimental results show that the proposed PTs not only have very low AC resistance and leakage inductance, but also generate extremely low levels of CM noise. Considering that the proposed PT has inter-winding capacitance equal to 700pF, it is very interesting to see that it generates significantly less CM noise than does a traditional wire-wound transformer that has only 10pF parasitic capacitance. Therefore, the proposed method gives designers the opportunity to minimize AC resistance and leakage inductance by using highly inter-leaved structures, without having to worry about CM noise caused by large inter-winding capacitance.
[Non-penetrating deep sclerectomy combined with a collagen implant in primary open-angle glaucoma. Medium-term retrospective results].

PURPOSE To evaluate the middle term tonometric results of a new filtering procedure, the non penetrating deep sclerectomy with collagen device, in primary open-angle glaucoma. This technique aims to eliminate or minimize the complications of classical trabeculectomy. MATERIAL AND METHOD This procedure has been developed by Koslov et al. Under a limbal-base conjunctival flap and a superficial scleral flap, the ablation of a deep scleral flap takes away the external wall of Schlemm's canal, leaving only the Descemet membrane. A visible filtration across the opened Schlemm's canal and Descemet membrane is obtained. To improve the aqueous filtration, a cylindric collagen device, made from biocompatible porcine scleral tissue, known for its high water content, is fixed in the deep scleral bed with a 10/0 nylon suture. This device provides a support for the elimination route of aqueous humor and acts like a sponge, carrying the liquid by capillary action. It is sterilized by irradiation. Full guarantee against viral contamination is provided. This procedure ends in one suture (40/0 nylon) of superficial scleral flap and conjunctival closing suture. We conducted a retrospective study. Our material included 159 patients (92 males, 65 females), 2/9 eyes. The mean age was 65 years (11-91). The mean follow-up : 8 months (3-20). The types of glaucoma were: POAG: 183 eyes; juvenile POAG: 18 eyes: pigmentary glaucoma: 11 eyes; capsular glaucoma: 7 eyes, 58 eyes (40 patients) presented one or several risk factors of failure for filtering surgery. RESULTS The mean pre-operative IOP was 24 mmHg +/- 6.60; 15.7 +/- 5.30 at the end of the follow-up (delta average IOP: 9.1 +/- 7.1). The probability success rate (IOP < or = 20 mmHg), according to the Kaplan-Meier Method, was 89% at six months, 75.6% at 16 months. With monotherapy with beta blockers, 79% at 16 months. It was better in the without risk factors group. The mean change in visual acuity was inferior to 0.1 at the end of the follow-up. Except several hyphemas, no complications of the trabeculectomy were observed. The reelevation of IOP was due to an internal obstruction (goniosynechiae or bad filtration), it was treated with Nd-Yag laser with a 2/3 of success rate. External obstruction was treated by 5FU injections into the bleb. CONCLUSION Non penetrating deep sclerectomy with collagen device can be an excellent alternative to trabeculectomy in open and wide angles. It does not modify visual actuity. It carries less complications than trabeculectomy and the use of antimitotic agents is safer.
Network Coded Cooperative BICM-OFDM

In this paper, we study a cooperative diversity scheme for wireless systems employing network coding and the combination of bit-interleaved coded modulation (BICM) and orthogonal frequency division multiplexing (OFDM). The considered system comprises multiple sources, one relay, and one destination. The relay decodes the signal received from all sources and performs network coding before forwarding the signal to the destination. We propose a simple cooperative maximum-ratio combining scheme for decoding at the destination which can successfully exploit the full spatial and frequency diversity offered by the channel for arbitrary number of sources and arbitrary modulation schemes. We derive a closed-form upper bound for the asymptotic worst-case pairwise error probability and the diversity gain of the considered network coded cooperative BICM-OFDM scheme. Simulation results corroborate the derived diversity gain and show the effectiveness of a low complexity decoding scheme.
Predicting Query Quality for Applications of Text Retrieval to Software Engineering Tasks

Context: Since the mid-2000s, numerous recommendation systems based on text retrieval (TR) have been proposed to support software engineering (SE) tasks such as concept location, traceability link recovery, code reuse, impact analysis, and so on. The success of TR-based solutions highly depends on the query submitted, which is either formulated by the developer or automatically extracted from software artifacts. Aim: We aim at predicting the quality of queries submitted to TR-based approaches in SE. This can lead to benefits for developers and for the quality of software systems alike. For example, knowing when a query is poorly formulated can save developers the time and frustration of analyzing irrelevant search results. Instead, they could focus on reformulating the query. Also, knowing if an artifact used as a query leads to irrelevant search results may uncover underlying problems in the query artifact itself. Method: We introduce an automatic query quality prediction approach for software artifact retrieval by adapting NL-inspired solutions to their use on software data. We present two applications and evaluations of the approach in the context of concept location and traceability link recovery, where TR has been applied most often in SE. For concept location, we use the approach to determine if the list of retrieved code elements is likely to contain code relevant to a particular change request or not, in which case, the queries are good candidates for reformulation. For traceability link recovery, the queries represent software artifacts. In this case, we use the query quality prediction approach to identify artifacts that are hard to trace to other artifacts and may therefore have a low intrinsic quality for TR-based traceability link recovery. Results: For concept location, the evaluation shows that our approach is able to correctly predict the quality of queries in 82% of the cases, on average, using very little training data. In the case of traceability recovery, the proposed approach is able to detect hard to trace artifacts in 74% of the cases, on average. Conclusions: The results of our evaluation on applications for concept location and traceability link recovery indicate that our approach can be used to predict the results of a TR-based approach by assessing the quality of the text query. This can lead to saved effort and time, as well as the identification of software artifacts that may be difficult to trace using TR.
The Application of Credit Risk Models to Macroeconomic Scenario Analysis and Stress Testing

The application of credit risk models in Comprehensive Capital Analysis and Review and European Banking Authority mandated regulatory macroeconomic stress testing is of significant concern for banks. The credit models that are used to project stressed losses and impairments under multi-horizon macroeconomic scenarios are also instrumental in projecting interest income and accrual as well as the balances that go into projected risk-weighted assets. In this paper we demonstrate how different credit risk models can be efficiently implemented for scenario analysis and stress testing execution with concrete application examples. Many of the credit risk models banks use in practice can be efficiently implemented through a very simple conditional Markov iteration. Examples include multi-factor models derived from the Merton structural approach and dynamic transition matrix models that depend on economic factors and are traditionally estimated on cohorts of loans. We also analyse the efficient implementation of more complex dynamic transition matrix models with the added feature of delinquency (rating) history tracking. Such models are frequently used for both retail and corporate portfolios and can introduce significant past state dependence. Traditionally, such models are therefore deployed in scenario analysis and stress testing using simulation of state transitions. However, in some important cases, such as quarterly models and monthly models with delinquency state indicator functions, the models can be solved more efficiently with an expanded conditional Markov iteration.
Particle-Based Message Passing Algorithm for Inference Problems in Wireless Sensor Networks

Optimal distributed estimation algorithms are usually not practical for wireless sensor networks (WSNs). This is because, in a general setup, these algorithms have high computational and data communication costs. Thus, sub-optimal algorithms that use quantized data and are based on linear and Gaussian approximations have been proposed in the literature. Such approximations are not always applicable. In this paper, we propose a distributed estimation method based on the well-known sum-product algorithm. To maintain a feasible complexity for WSNs, the sum-product update rules are reformulated using particle filtering. We consider the problem of distributed target tracking based on quantized data in a WSN. After deriving the factor graph representation of this tracking problem, we apply our proposed algorithm. We then study its performance based on the number of quantization bits, the number of particles and the measurement noise.
Brain glucose metabolism in diffuse large B-cell lymphoma patients as assessed with FDG-PET: impact on outcome and chemotherapy effects

Background There is a lack of data on the effect of rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) therapy on brain glucose metabolism of diffuse large B-cell lymphoma (DLBCL) patients, as measured by 18F-fluoro-2-deoxy-D-glucose positron emission tomography (FDG-PET). Moreover, the prognostic value of brain glucose metabolism measurements is currently unknown. Purpose To investigate the use of FDG-PET for measurement of brain glucose metabolism in R-CHOP-treated DLBCL patients, and to assess its prognostic value. Material and Methods This retrospective study included DLBCL patients who underwent FDG-PET including the brain. FDG-PET metabolic volume products (MVPs) of the entire brain, cerebral cortex, basal ganglia, and cerebellum were measured, before and after R-CHOP therapy. Whole-body total lesion glycolysis (TLG) was also measured. Results Thirty-eight patients were included, of whom 18 had an appropriate end-of-treatment FDG-PET scan. There were no significant differences (P > 0.199) between pre- and post-treatment brain glucose metabolism metrics. Low basal ganglia MVP was associated with a significantly worse progression-free survival (PFS) and overall survival (OS) (P = 0.020 and P = 0.032), and low cerebellar MVP was associated with a significantly worse OS (P = 0.034). There were non-significant very weak correlations between pretreatment brain glucose metabolism metrics and TLG. In the multivariate Cox regression, only the National Comprehensive Cancer Network International Prognostic Index (NCCN-IPI) remained an independent predictor of PFS (hazard ratio 3.787, P = 0.007) and OS (hazard ratio 2.903, P = 0.0345). Conclusion Brain glucose metabolism was not affected by R-CHOP therapy. Low pretreatment brain glucose metabolism was associated with a worse outcome, but did not surpass the predictive value of the NCCN-IPI.
Interleukin-6 and C-Reactive Protein Levels and 9-Year Cognitive Decline in Community-Dwelling Older Women: The Women's Health and Aging Study II.

BACKGROUND Elevated inflammation is a proposed mechanism relating chronic diseases to cognitive dysfunction. The objective of this study was to test the hypothesis that greater levels of inflammation, as measured by the proinflammatory cytokine interleukin-6 (IL-6) and C-reactive protein, are associated with faster rates of cognitive decline among cognitively intact community-dwelling older women. METHODS We analyzed 336 women from the Women's Health and Aging Study II. Cognitive assessments were performed at baseline and every 18-36 months, and included the following domains: immediate and delayed memory (Hopkins Verbal Learning Test), psychomotor speed (Trail Making Test, Part A), and executive function (Trail Making Test, Part B). Aggregate measures of IL-6 and C-reactive protein, based on the average from visits one and two, were analyzed categorically. Random effects models were employed to test the relationship between tertiles of each inflammatory marker and changes in cognitive domain scores over 9 years. RESULTS Moderate and high levels of IL-6 predicted early declines in psychomotor speed by 1.0 connection/min per year. There were no differences in baseline scores or rates of change across tertiles of IL-6 in memory or executive function. No differences were observed across tertiles of C-reactive protein for all cognitive domains. CONCLUSIONS Higher levels of serum IL-6 were associated with greater declines in psychomotor speed over 9 years. This finding could suggest that elevated IL-6 may result in microvascular changes that may lead to damage of myelin sheaths that line neuronal axons, leading to decreased neuron propagation and impaired processing speed; however, mechanistic studies are needed to evaluate these hypotheses.
Reductions in Intraocular Pressure After Acute Aerobic Exercise: A Meta-Analysis

Objective:Aerobic exercise is known to reduce elevated intraocular pressure (IOP), a primary risk factor for a disease of the eye known as primary open-angle glaucoma. Given the disparate nature of experimental protocols across the literature, an analysis of studies on the effect of acute aerobic exercise on IOP is necessary to verify the influence of participant characteristics, exercise intensity, and duration. Data Sources:The electronic databases PubMed, Web of Science, and Embase were searched, producing 35 empirical studies for review. Ten studies producing 14 independent groups were chosen as per the criteria of the analysis. Main Results:Random effects model was used to produce subgroup analyses, and meta-regressions were used to verify the impact of group allocation, intensity, and duration on the interstudy variability of the effect size (ES). The outcome variable of postexercise change in IOP produced a significant effect of exercise, almost 2-fold greater for sedentary populations than for normally active populations (ES = −4.198; confidence interval, −5.151 to −3.245); ES = −2.340; confidence interval, −3.305 to 1.375, respectively). The significant effect of exercise on IOP is potentially mediated by group allocation. Intensity and duration do not contribute to the overall ES nor do they explain the difference between sedentary and normally active populations. Conclusions:There is a robust effect of exercise on IOP for sedentary participants. However, the heterogeneity across study parameters, such as exercise protocol, IOP measurement, and participant selection, prohibited the inclusion of studies in this analysis that may have influenced the results. The current analysis makes clear the need for standardization of protocol across this field of research.
Recurrent seizures may cause hippocambal damage in temporal lobe epilepsy

Objective: To investigate whether recurrent seizures cause hippocampal damage in temporal lobe epilepsy (TLE). Patients: Eighteen patients with newly diagnosed cryptogenic TLE, 14 patients with chronic well-controlled cryptogenic TLE, 32 patients with chronic drug-resistant cryptogenic TLE, and 25 healthy subjects were studied. Measurements: Hippocampal MRI volumetry and T2 relaxometry were used. Results: Chronic drug-resistant patients with seizure focus in the left temporal lobe had an 18% smaller left hippocampus and chronic drug-resistant patients with seizure focus in the right temporal lobe had a 14% smaller right hippocampus than did the control group (p < 0.05). Chronic drug-resistant patients with seizure focus on the left side had longer T2 relaxation times in the body of the left hippocampus than did the control group (p < 0.001) and chronic drug-resistant patients with seizure focus on the right side had longer T2 relaxation times in the body of the right hippocampus than did the control subjects (p < 0.01). In all patients with a left seizure focus, the left hippocampal volume correlated inversely with the estimated total number of partial (r= -0.391, p < 0.01) or generalized (r = -0.312, p < 0.05) seizures the patient had experienced. The prolongation of the left T2 relaxation time in the body of the hippocampus correlated with the total number of both partial (r = 0.670, p < 0.001) and generalized (r = 0.481, p< 0.001) seizures and with the duration of TLE symptoms (r = 0.580, p < 0.001). Conclusions: In patients with cryptogenic epilepsy, recurrent seizures may cause damage to the hippocampus throughout the lifetime of the patient.
A Baeyer-Villiger Oxidation Specifically Catalyzed by Human Flavin-Containing Monooxygenase 5

10-((4-Hydroxypiperidin-1-yl)methyl)chromeno[4,3,2-de]phthalazin-3(2H)-one (E7016), an inhibitor of poly(ADP-ribose) polymerase, is being developed for anticancer therapy. One of the major metabolites identified in preclinical animal studies was the product of an apparent oxidation and ring opening of the 4-hydroxypiperidine. In vitro, this oxidized metabolite could not be generated by incubating E7016 with animal or human liver microsomes. Further studies revealed the formation of this unique metabolite in hepatocytes. In a NAD(P)+-dependent manner, this metabolite was also generated by liver S9 fractions and recombinant human flavin-containing monooxygenase (FMO) 5 that was fortified with liver cytosol fractions. In animal and human liver S9, this metabolic pathway could be inhibited by 4-methylpyrazole, bis-p-nitrophenylphosphate (BNPP), or a brief heat treatment at 50°C. Based on these results, the overall metabolic pathway was believed to involve a two-step oxidation process: dehydrogenation of the secondary alcohol in liver cytosol followed by an FMO5-mediated Baeyer-Villiger oxidation in liver microsomes. The two oxidation steps were coupled via regeneration of NAD(P)+ and NAD(P)H. To further confirm this mechanism, the proposed ketone intermediate was independently synthesized. In an NAD(P)H-dependent manner, the synthetic ketone intermediate was metabolized to the same ring-opened metabolite in animal and human liver microsomes. This metabolic reaction was also inhibited by BNPP or a brief heat treatment at 50°C. Methimazole, the substrate/inhibitor of FMO1 and FMO3, did not inhibit this reaction. The specificity of FMO5 toward catalyzing this Baeyer-Villiger oxidation was further demonstrated by incubating the synthetic ketone intermediate in recombinant enzymes.