Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling risk stratification in human cancer

MOTIVATION Despite huge prognostic promises, gene expression-based survival assessment is rarely used in clinical routine. Main reasons include difficulties in performing and reporting analyses and restriction in most methods to one high-risk group with the vast majority of patients being unassessed. The present study aims at limiting these difficulties by (i) mathematically defining the number of risk groups without any a priori assumption; (ii) computing the risk of an independent cohort by considering each patient as a new patient incorporated to the validation cohort and (iii) providing an open-access Web site to freely compute risk for every new patient. RESULTS Using the gene expression profiles of 551 patients with multiple myeloma, 602 with breast-cancer and 460 with glioma, we developed a model combining running log-rank tests under controlled chi-square conditions and multiple testing corrections to build a risk score and a classification algorithm using simultaneous global and between-group log-rank chi-square maximization. For each cancer entity, we provide a statistically significant three-group risk prediction model, which is corroborated with publicly available validation cohorts. CONCLUSION In constraining between-group significances, the risk score compares favorably with previous risk classifications. AVAILABILITY Risk assessment is freely available on the Web at https://gliserv.montp. inserm.fr/PrognoWeb/ for personal or test data files. Web site implementation in Perl, R and Apache.
Potency of Fish Collagen as a Scaffold for Regenerative Medicine

Cells, growth factors, and scaffold are the crucial factors for tissue engineering. Recently, scaffolds consisting of natural polymers, such as collagen and gelatin, bioabsorbable synthetic polymers, such as polylactic acid and polyglycolic acid, and inorganic materials, such as hydroxyapatite, as well as composite materials have been rapidly developed. In particular, collagen is the most promising material for tissue engineering due to its biocompatibility and biodegradability. Collagen contains specific cell adhesion domains, including the arginine-glycine-aspartic acid (RGD) motif. After the integrin receptor on the cell surface binds to the RGD motif on the collagen molecule, cell adhesion is actively induced. This interaction contributes to the promotion of cell growth and differentiation and the regulation of various cell functions. However, it is difficult to use a pure collagen scaffold as a tissue engineering material due to its low mechanical strength. In order to make up for this disadvantage, collagen scaffolds are often modified using a cross-linker, such as gamma irradiation and carbodiimide. Taking into account the possibility of zoonosis, a variety of recent reports have been documented using fish collagen scaffolds. We herein review the potency of fish collagen scaffolds as well as associated problems to be addressed for use in regenerative medicine.
A model of temporal response properties in primary auditory cortex

The temporal response properties of cells in primary auditory cortex differ markedly from those observed sub-cortically, in particular the ability to synchronise firing to amplitude modulations is restricted to modulations below 10-20 Hz (Schreiner et al 1997). In the thalamocortical transformation of incoming signals a great deal of the temporal fine structure is lost (Creutzfeldt et al 1980), and the effects of a masker on a probe tone can be detected up to 400 ms after masker offset (Brosch and Schreiner 1997). What gives rise to these phenomena and can they be explained by some common mechanism? Explanations in terms of intracortical inhibitory circuits have been proposed but inhibition does not provide an adequate account, at least in the case of forward masking which is unaffected by the application of a GABA antagonist. On the other hand, simple threshold neural models cannot replicate such behaviour without some form of inhibition. The purpose of this investigation was to explore to what extent synaptic depression at thalamocortical synapses could account for the temporal response properties observed in primary auditory cortex. A model of synaptic depression is described and its behaviour investigated in a number of experiments. The model is shown to successfully replicate many experimental observations. In addition, the model also provides a novel account of the effect of subthreshold stimuli.
A 0.22 nJ/b/iter 0.13 μm turbo decoder chip using inter-block permutation interleaver

This paper presents a high speed turbo decoder containing 32 MAP decoders with a inter-block permutation interleaver. The proposed butterfly network guarantees contention-free property and promises parallel processing of turbo decoder without performance degradation. In addition, our approach also features a relocated radix-2 x 2 ACS structure to reduce the critical path delay. After manufacturing by 0.13 μm CMOS process, the test results show the energy efficiency is 0.22 nJ/b/iter in the 160 Mb/s data rate.
The Cross Section of Jumps around Earnings Announcements

Jump dynamics vary greatly across stocks. However, little is known about the causes of such variations and their associations to various firm characteristics. Controlling for information shocks from quarterly earnings announcements, we examine cross-sectional determinants of jumps in stock prices and nd that small, illiquid, and growth firms with high trading volume, high turnover, and low return volatility are more susceptible to jumps. Moreover, the magnitude of jumps decreases with firm size, liquidity, return volatility, and book-to-market ratio, but increases with pre-announcement trading volume and turnover. The results are robust to alternative model specifications and estimation methods.
Robust Taylor Rules in an Open Economy with Heterogeneous Expectations and Least Squares Learning

This thesis consists of four papers, of which paper 1 and 4 are co-written with Mikael Bask. Paper [1] implements chartists trading in a sticky-price monetary model for determining the exchange rate. It is demonstrated that chartists cause the exchange rate to "overshoot the overshooting equilibrium" of a sticky-price monetary model. Chartists base their trading on a short-long moving average. The importance of technical trading depends inversely on the time horizon in currency trade. The exchange rate's perfect foresight path near long-run equilibrium is derived and it is demonstrated that the shorter the time horizon, the greater the exchange rate overshooting. The aim of Paper [2] is to see how the dynamics of the basic target zone model changes when chartists and fundamentalists are introduced. Chartists use technical trading and the relative importance of technical and fundamental analyses depend on the time horizon in currency trade. The model also includes realignment expectations, which increase with the weight of chartists. The introduction of chartists may significantly reduce and reverse, the so-called "honeymoon effect" of a fully credible target zone. Further, chartists may cause the correlation between the exchange rate and the instantaneous interest rate differential to become either positive or negative. Using a chartist-fundamentalist set-up, Paper [3] derives the effects on the current exchange rate of central bank intervention. Fundamentalists have rational expectations and chartists use so called support and resistance levels in their trading. This technique results in chartists having both bandwagon expectations and regressive expectations. Chartists may enhance or suppress the effect of intervention depending on their expectations. The results indicate that a chartist channel exists. The aim of Paper [4] is threefold; (i) to investigate if there is a unique rational expectations equilibrium (REE) in a new Keynesian macroeconomic model augmented with technical trading, (ii), to investigate if the unique REE is adaptively learnable and, (iii), to investigate if this unique and adaptively learnable REE is desirable in an inflation rate targeting regime. The monetary authority is using a Taylor rule when setting the interest rate. A main conclusion is that a robust Taylor rule implies that the monetary authority should increase (decrease) the interest rate when the CPI inflation rate increases (decreases) and when the currency gets stronger (weaker).
Cross-cultural adaptation and psychometric properties of an Arabic language version of the Brief Illness Perception Questionnaire in Lebanon

Background Patients’ positive illness perceptions (IPs) significantly contribute to treatment success. The Brief Illness Perception Questionnaire (Brief IPQ) is widely used in various diseases for assessing IPs. It was developed in English-speaking countries and studies on it in Arab countries are scarce. Objectives, Setting and design This observational cross-sectional study aimed to cross-culturally adapt the Brief IPQ English version into a modern Arabic language version and determine its psychometric properties in a sample of Lebanese cardiac disease patients. This study was approved by the Institutional Review Board of Saint Joseph University of Beirut, Lebanon. Participants A convenience sample of 30 patients with cardiac disease were recruited during routine visits to cardiologists’ offices in Beirut, Lebanon. Inclusion criteria were at least one cardiac disease for at least 6 months with no acute episode or exacerbation of the disease during the 6 preceding months, age≥18 years, and the ability to read and comprehend Arabic. The pre-final version of the Brief IPQ Arabic version was tested for face and content validity. The meaning, comprehensibility, and acceptability were studied by individual interviews. For discriminant validity and internal consistency of the Brief IPQ Arabic version (Brief IPQ-Ar), 100 patients were recruited in a similar manner using the same inclusion criteria. To assess reproducibility, 30 patients, selected randomly from the 100 patients, filled the questionnaire a second time, 3–4 weeks after its first administration and under the same conditions. Main outcome measures Psychometric properties of the Brief IPQ-Ar among Lebanese patients suffering from cardiac diseases. Results Semantic equivalence between the Brief IPQ-Ar questions and patients’ descriptions was 100%. Cronbach's alpha was 0.717, which shows good internal consistency. Reproducibility was satisfactory (ICC values>0.776). Moreover, the Brief IPQ-Ar discriminated participants according to the type of cardiac disease and treatment-related characteristics. Conclusions We confirm that the Brief IPQ-Ar is appropriate for exploring IPs in cardiac disease patients whose first language is Arabic. Further research should be conducted to test this Arabic version in other types of diseases.
Encoding and Decoding Cortical Representations of Tactile Features in the Vibrissa System

During behavior, rats and other rodents use their facial vibrissae to actively explore surfaces through whisking and head/body movement, resulting in complex sensory inputs that vary over a large range of angular velocities and temporal scales. How these complex sensory inputs manifest in the patterns of cortical firing events that ultimately form the perceptual experience is not well understood. Through single-unit cortical recordings of layer 4 neurons in S1 of the anesthetized rat, we systematically quantified the interactions between instantaneous velocity and timing of vibrissa motion, finding a strong interaction between angular velocity and timing of contacts on the tens of milliseconds time scale. From the quantification of these joint tuning properties, a detailed nonlinear encoding model was formulated that was highly predictive of firing probability and timing characteristics of the sparse cortical representation of complex patterned tactile inputs. Within a Bayesian framework, the encoding model was then used to decode tactile patterns under simple transformations of the stimulus along dimensions of velocity and timing, as a demonstration of the lower bound of the idealized perceptual capabilities of the animal.
The High Repeatability of Salient Regions

In this paper, we show that salient regions, detected by a biologically motivated attention system, have a considerably higher repeatability than features detected by standard detectors (Harris-Laplacians and DoG features). If a scene contains a salient region, which differs in one of several possible features from the rest of the scene, the repeatability is close to 100%. In settings in which no especially salient region is present, the repeatability of attention regions is similar to DoG features and considerably higher than Harris-Laplacians.
Dynamics of Effective Quotes and Spreads Between Consecutive Trades - A Real-Time Structural Model of Price Formation

This paper develops a real-time structural model of price formation, and uses it to investigate the dynamics of effective quotes and bid-ask spreads between consecutive trades. There is some evidence that the effective bid-ask spreads increase over time when no orders arrive. The effective quotes are found to change over time when no orders arrive. The dynamics of bid and ask are different and are related to the direction of previous transaction. Market makers act as though they believe that clustering trades with middle-range duration (coming one or two minutes after the last trades) are more likely to contain private information, while reversing trades with same duration are less likely to contain private information. Some stylized facts are also established regarding the average duration and frequency for clustering trades, reversing trades,upticks, and downticks.
Official Demand for US Debt: Implications for US Real Rates

We estimate a structural term-structure model in which arbitrageurs accommodate demand pressures exerted by domestic and foreign official investors. Demand pressures can affect real rates by altering the aggregate price of duration risk, and therefore through changes in the bond risk premia. We find that foreign official demand pressures contributed to reduce long-term real yields largely in the 2001-08 period, whereas the Fed mainly during the subsequent quantitative easing program. Fed pressures arise not only from the expansion of the Fed's balance sheet, but also from the extension of its maturity profile while keeping its size constant.
Predicting Inflation: Does the Quantity Theory Help?

Various inflation forecasting models are compared using a simulated out-of-sample forecasting framework. We focus on the question of whether monetary aggregates are useful for forecasting inflation, but unlike previous work we examine a wide range of forecast horizons and allow for estimated as well as theoretically specified cointegrating relationships in some of our models. Our findings indicate that there are forecasting gains from allowing monetary aggregates to enter into prediction models via cointegrating restrictions among money, prices, and output derived from a simple version of the quantity theory, but only when the cointegrating relations are specified a priori based on economic theory. When estimated cointegrating relations are used in a vector error correction (VEC) model, a vector autoregression (VAR) model in differences predicts better. These results hold, even during the 1990s, and evidence is presented suggesting that previous findings of a breakdown in the cointegrating relationship among prices, money, and output is the result of a failure of M2 as a measure of the money stock, and is not due to money demand instabilities. Two Monte Carlo experiments that lend credence to our findings are also reported on. The first shows that cointegration vector parameter estimation error is crucial when using VEC models for forecasting, and helps to explain previous findings of the failure of VEC models to forecast better than VAR models. The second shows that random walk and other atheoretical models routinely forecast better than correctly specified alternative models, due to parameter estimation error, indicating that caution needs to be exercised when interpreting the results of such comparisons, particularly when making statements concerning the usefulness of empirical models for use in policy-setting.
Nitrite reductase genes in halobenzoate degrading denitrifying bacteria.

Abstract Diversity of the functional genes encoding dissimilatory nitrite reductase was investigated for the first time in denitrifying halobenzoate degrading bacteria and in two 4-chlorobenzoate degrading denitrifying consortia. Nitrite reductase genes were PCR-amplified with degenerate primers (specific to the two different types of respiratory nitrite reductase, nirS and nirK), cloned and sequenced to determine which type of nitrite reductase was present in each isolate and consortium. Halobenzoate degrading isolates belonging to the genera Ochrobactrum, Ensifer and Mesorhizobium, as well as Pseudomonas mendocina CH91 were found to have nirK genes, which were closely related to the previously published nirK genes of Ochrobactrum anthropi, Achromobacter cycloclastes, Alcaligenes faecalis and Pseudomonas aureofaciens, respectively. The isolates assigned to the genera Acidovorax, Azoarcus and Thauera as well as all other species in the genera Thauera and Azoarcus contained nirS genes, which were closely related to the nirS genes from Pseudomonas stutzeri with some exceptions. In addition, only nirS genes were found in 4-chlorobenzoate degrading denitrifying consortia. Three different major terminal restriction fragments from the nirS genes were detected by terminal restriction fragment length polymorphism analysis of the consortia, and five different nirS genes were cloned from one consortium. Three nirS gene clones were closely related to nirS genes from Thauera chlorobenzoica, Azoarcus tolulyticus and Pseudomonas aeruginosa, respectively. The phylogeny of nir genes was not entirely congruent with the 16S rRNA phylogeny of the genera nor was it correlated with the ecological and geographical origins or isolation substrates used for isolation and enrichment of consortia.
Immunomodulation of Homeopathic Thymulin 5CH in a BCG-Induced Granuloma Model

The present study analyzed the immune modulation mechanisms of thymulin 5CH in a granuloma experimental model. Male adult Balb/c mice were inoculated with BCG into the footpad to induce granuloma, which was quantitatively evaluated. The phenotypic characterization of phagocyte, T- and B-lymphocyte populations in the peritoneum, and local lymph node was done by flow cytometry. During all experimental periods, thymulin 5CH and vehicle (control) were given ad libitum to mice, diluted into the drinking water (1.6 × 10−17 M). After 7 days from inoculation, thymulin-treated mice presented reduction in the number of epithelioid cytokeratine-positive cells (P = 0.0001) in the lesion, in relation to young phagocytes. After 21 days, the differentiation of B1 peritoneal stem cells into phagocytes reached the peak, being higher in thymulin-treated mice (P = 0.0001). Simultaneously, the score of infected phagocytes in the lesion decreased (P = 0.001), and the number of B1-derived phagocytes, CD4+ and CD8+ T lymphocytes in the local lymph node increased in relation to control (P = 0.0001). No difference was seen on the CD25+ Treg cells. The results show that thymulin 5CH treatment is able to improve the granuloma inflammatory process and the infection remission, by modulating local and systemic phagocyte differentiation.
Natural History of Cardiovascular Disease in Patients With Diabetes

Atherosclerotic vascular disease is more common in diabetic than in nondiabetic individuals. Diabetic macrovascular disease also has a more severe course with greater prevalence of multiple-vessel coronary artery disease and more diffuse elongated atheromas in affected blood vessels. In this review, we discuss possible reasons for increased incidence of cardiovascular (CV) events in individuals with diabetes. Although an increased prevalence of standard CV risk factors has been clearly documented in association with diabetes, diabetes-related abnormalities, particularly hyperglycemia, also play an important role. Epidemiological studies suggest that the effect of hyperglycemia on CV risk is independent of other known risk factors, but no data from primary interventional trials are available yet. Analysis of datasets from populations that included individuals with impaired glucose tolerance and impaired fasting glucose suggest that the pathogenic role of hyperglycemia on the blood vessel wall already exists in the early stages of glucose intolerance. The effect of postprandial or postchallenge hyperglycemia seems to be greater than the effect of fasting blood glucose abnormalities. The relationship of postprandial glycemia, fasting blood glucose, and CV risk in individuals with diagnosed (or overt) diabetes is less clear, although most reports indicate a greater pathogenic potential of postprandial hyperglycemia rather than fasting hyperglycemia. Based on the results of epidemiological reports, the most appropriate targets in interventional trials are postprandial hyperglycemia or A1C.
Pyrosequencing-Based Analysis of the Mucosal Microbiota in Healthy Individuals Reveals Ubiquitous Bacterial Groups and Micro-Heterogeneity

This study used 16S rRNA-based pyrosequencing to examine the microbial community that is closely associated with the colonic mucosa of five healthy individuals. Spatial heterogeneity in microbiota was measured at right colon, left colon and rectum, and between biopsy duplicates spaced 1 cm apart. The data demonstrate that mucosal-associated microbiota is comprised of Firmicutes (50.9%±21.3%), Bacteroidetes (40.2%±23.8%) and Proteobacteria (8.6%±4.7%), and that interindividual differences were apparent. Among the genera, Bacteroides, Leuconostoc and Weissella were present at high abundance (4.6% to 41.2%) in more than 90% of the studied biopsy samples. Lactococcus, Streptococcus, Acidovorax, Acinetobacter, Blautia, Faecalibacterium, Veillonella, and several unclassified bacterial groups were also ubiquitously present at an abundance <7.0% of total microbial community. With the exception of one individual, the mucosal-associated microbiota was relatively homogeneous along the colon (average 61% Bray-Curtis similarity). However, micro-heterogeneity was observed in biopsy duplicates within defined colonic sites for three of the individuals. A weak but significant Mantel correlation of 0.13 was observed between the abundance of acidomucins and mucosal-associated microbiota (P-value = 0.04), indicating that the localized biochemical differences may contribute in part to the micro-heterogeneity. This study provided a detailed insight to the baseline mucosal microbiota along the colon, and revealed the existence of micro-heterogeneity within defined colonic sites for certain individuals.
Adaptive Carrier Synchronization Using Decision-Aided Kalman Filtering Algorithms

A new adaptive carrier recovery algorithm is proposed by using the decision-aided extended Kalman filtering technique. In order to reduce computational complexity of the Kalman recursions, the state model in the new algorithm uses only phase rather than both phase and frequency which are usually used in conventional modeling. The frequency is considered as an input term to the system equation and estimated by a phase error detector. A reduced observation model is also introduced to relieve computing load from multiple matrix to scalar operations in the Kalman recursions. Simulations show that the proposed one-state Kalman algorithm has better performance and lower complexity than the two-state Kalman algorithm for synchronization applications. The new algorithm is applied to the cable modem downstream system to demonstrate its effectiveness with FPGA implementation results.