Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting epileptic electroencephalogram by Recurrence Quantification Analysis

Aiming at studying the influences of epilepsy on brain's nonlinear characteristics, we analyzed the difference between the normal EEG (electroencephalogram) and epileptic EEG from the perspective of nonlinear dynamics. Two sets of data used in this paper, including 16 cases of normal EEG and the same quantity of epileptic EEG, were from General Hospital of Nanjing Military Region. Firstly, on the basis of the Recurrence Plot (RP), the Order Recurrence Plot (ORP) was adopted to analyze two different kinds of EEG qualitatively. Then Average Diagonal Length, a parameter coming from Recurrence Quantification Analysis (RQA), was calculated to analyze the difference between normal EEG and epileptic EEG in nonlinear character, quantitatively. Compared with the healthy control subjects, the epileptic EEG is more regular and more certain, meanwhile, it's Average Diagonal Length is longer. Epilepsy makes patients' EEG become weaker in nonlinear chaotic characteristics but stronger in regularity and certainty.
A pilot study on automatic inference rule discovery from Turkish text

In this paper we present a framework for extraction of inference rules from Turkish documents, such as "A solved B ~ A found a solution to B". Many natural language processing tasks, such as question answering, information retrieval and machine translation can benefit tremendously from inference rules. Our framework consists of three layers: construction of dependency trees; determining predicates and their complements and finally discovery of inference rules via clustering. We use Silhouette Index (SI) of the clusters as an automatic evaluation metric.
Ex Vivo Host and Parasite Response to Antileishmanial Drugs and Immunomodulators

Background Therapeutic response in infectious disease involves host as well as microbial determinants. Because the immune and inflammatory response to Leishmania (Viannia) species defines the outcome of infection and efficacy of treatment, immunomodulation is considered a promising therapeutic strategy. However, since Leishmania infection and antileishmanial drugs can themselves modulate drug transport, metabolism and/or immune responses, immunotherapeutic approaches require integrated assessment of host and parasite responses. Methodology To achieve an integrated assessment of current and innovative therapeutic strategies, we determined host and parasite responses to miltefosine and meglumine antimoniate alone and in combination with pentoxifylline or CpG 2006 in peripheral blood mononuclear cells (PBMCs) of cutaneous leishmaniasis patients. Parasite survival and secretion of TNF-α, IFN-γ, IL-10 and IL-13 were evaluated concomitantly in PBMCs infected with Luc-L. (V.) panamensis exposed to meglumine antimoniate (4, 8, 16, 32 and 64 μg SbV/mL) or miltefosine (2, 4, 8, 16 and 32 μM HePC). Concentrations of 4 μM of miltefosine and 8 μg SbV/mL were selected for evaluation in combination with immunomodulators based on the high but partial reduction of parasite burden by these antileishmanial concentrations without affecting cytokine secretion of infected PBMCs. Intracellular parasite survival was determined by luminometry and cytokine secretion measured by ELISA and multiplex assays. Principal Findings Anti- and pro-inflammatory cytokines characteristic of L. (V.) panamensis infection were evaluable concomitantly with viability of Leishmania within monocyte-derived macrophages present in PBMC cultures. Both antileishmanial drugs reduced the parasite load of macrophages; miltefosine also suppressed IL-10 and IL-13 secretion in a dose dependent manner. Pentoxifylline did not affect parasite survival or alter antileishmanial effects of miltefosine or meglumine antimoniate. However, pentoxifylline diminished secretion of TNF-α, IFN-γ and IL-13, cytokines associated with the outcome of infection by species of the Viannia subgenus. Exposure to CpG diminished the leishmanicidal effect of meglumine antimoniate, but not miltefosine, and significantly reduced secretion of IL -10, alone and in combination with either antileishmanial drug. IL-13 increased in response to CpG plus miltefosine. Conclusions and Significance Human PBMCs allow integrated ex vivo assessment of antileishmanial treatments, providing information on host and parasite determinants of therapeutic response that may be used to tailor therapeutic strategies to optimize clinical resolution.
Three-dimensional 1060-nm OCT: choroidal thickness maps in normal subjects and improved posterior segment visualization in cataract patients.

PURPOSE To evaluate the performance and potential clinical role of three-dimensional (3D) 1060-nm OCT by generating choroidal thickness (ChT) maps in patients of different ages with different degrees of ametropia and axial lengths and to investigate the effect of cataract grade on OCT retinal imaging quality. METHODS Axial lengths (ALs) and 45° fundus photographs were acquired from 64 eyes (34 healthy subjects, 19 to 80 years, ametropia +3 to -10 D). 3D 1060-nm OCT was performed over a 36° × 36° field of view with ∼7-μm axial resolution and up to 70 frames/s (512 A-scans/frame). ChT maps between retinal pigment epithelium and the choroidal-scleral interface, were generated and statistically analyzed. A further 30 eyes (19 subjects), with cataracts assessed with the LOCS III scale, were imaged with 3D 1060-nm OCT and 800-nm OCT, and visualization of the posterior segment was compared qualitatively. RESULTS In 64 eyes, ChT maps displayed a thickness decrease with increasing AL. Subfoveal ChT was 315 ± 106 μm (mean ± SD), negatively correlated with AL (R(2) = -0.47, P < 0.001). Averaged ChT maps of eyes with AL < 23.39 mm showed an increased ChT in an area ∼1500 μm inferior, compared with subfoveal ChT. Eyes with AL > 24.5 mm showed a larger variation and a thicker ChT superiorly than inferiorly. Reduced signal strength in cataractous eyes was found in 65% of the 800-nm OCT images, but in only 10% of the 1060-nm OCT images. CONCLUSIONS The imaging performance of 3D 1060-nm OCT is unique, producing maps that show the variation in ChT over the entire field of view, in relation to axial length. This imaging system has the potential of visualizing a novel clinical diagnostic biomarker. Compared with 800-nm OCT, it provides superior visualization of the posterior pole in cataractous eyes.
A role for p75 neurotrophin receptor in the control of apoptosis‐driven hair follicle regression

To examine the mechanisms that underlie the neurotrophin‐induced, apoptosis‐driven hair follicle involution (catagen), the expression and function of p75 neurotrophin receptor (p75NTR), which is implicated in apoptosis control, were studied during spontaneous catagen development in murine skin. By RT‐PCR, high steady‐state p75NTR mRNA skin levels were found during the anagen– catagen transition of the hair follicle. By immunohistochemistry, p75NTR alone was strongly expressed in TUNEL+/Bcl2— keratinocytes of the regressing outer root sheath, but both p75NTR and TrkB and/or TrkC were expressed by the nonregressing TUNEL‐/Bcl2+ secondary hair germ keratinocytes. To determine whether p75NTR is functionally involved in catagen control, spontaneous catagen development was compared in vivo between p75NTR knockout (— /—) and wild‐type mice. There was significant catagen retardation in p75NTR knockout mice as compared to wild‐type controls (P<0.05). Instead, transgenic mice‐overexpressing NGF (promoter: K14) showed substantial acceleration of catagen (P<0.001). Although NGF, brain‐derived neurotrophic factor (BDNF), and neurotrophin 3 (NT‐3) accelerated catagen in the organ‐cultured skin of C57BL/6 mice, these neurotrophins failed to promote catagen development in the organ‐cultured p75NTR null skin. These findings suggest that p75NTR signaling is involved in the control of kerotinocyte apoptosis during catagen and that pharmacological manipulation of p75NTR signaling may prove useful for the treatment of hair disorders that display premature entry into catagen. —Botchkarev, V. A. , Botchkareva, N. V. , Albers, K. M. , Chen, L. ‐H. , Welker, P., Paus, R. A role for p75 neurotrophin receptor in the control of apoptosisdriven hair follicle regression. FASEB J. 14, 1931–1942 (2000)
New bounds for multi-dimensional packing

New upper and lower bounds are presented for a multi-dimensional generalization of bin packing called box packing.Several variants of this problem, including bounded space box packing, square packing, variable sized box packing and resource augmented box packing are also studied. The main results, stated for d = 2, are as follows: A new upper bound of 2.66013 for online box packing, a new 14/9 + ε polynomial time offline approximation algorithm for square packing, a new upper bound of 2.43828 for online square packing, a new lower bound of 1.62176 for online square packing, a new lower bound of 2.28229 for bounded space online square packing and a new upper bound of 2.32571 for online two-sized box packing.
Fluorescence changes reveal kinetic steps of muscarinic receptor–mediated modulation of phosphoinositides and Kv7.2/7.3 K+ channels

G protein–coupled receptors initiate signaling cascades. M1 muscarinic receptor (M1R) activation couples through Gαq to stimulate phospholipase C (PLC), which cleaves phosphatidylinositol 4,5-bisphosphate (PIP2). Depletion of PIP2 closes PIP2-requiring Kv7.2/7.3 potassium channels (M current), thereby increasing neuronal excitability. This modulation of M current is relatively slow (6.4 s to reach within 1/e of the steady-state value). To identify the rate-limiting steps, we investigated the kinetics of each step using pairwise optical interactions likely to represent fluorescence resonance energy transfer for M1R activation, M1R/Gβ interaction, Gαq/Gβ separation, Gαq/PLC interaction, and PIP2 hydrolysis. Electrophysiology was used to monitor channel closure. Time constants for M1R activation (<100 ms) and M1R/Gβ interaction (200 ms) are both fast, suggesting that neither of them is rate limiting during muscarinic suppression of M current. Gαq/Gβ separation and Gαq/PLC interaction have intermediate 1/e times (2.9 and 1.7 s, respectively), and PIP2 hydrolysis (6.7 s) occurs on the timescale of M current suppression. Overexpression of PLC accelerates the rate of M current suppression threefold (to 2.0 s) to become nearly contemporaneous with Gαq/PLC interaction. Evidently, channel release of PIP2 and closure are rapid, and the availability of active PLC limits the rate of M current suppression.
The Equity Home Bias: Contrasting an Institutional with a Behavioral Explanation

An empirically well-established finding is that equity portfolios are concentrated in the domestic equity market of the investor. Previous theoretical and empirical analyses have mainly focused on institutional explanations and largely neglected individual behavior. In this study we report the results of an experiment in which we contrast institutional with behavioral explanations by comparing asymmetric information to social identity. Our results show that social forces, triggered by group affiliation, drive underdiversified and domestically biased portfolio allocations. Moreover, social identity explains the observed behavior equally well as asymmetric information. We also find that individuals are spuriously more optimistic toward the performance of domestic firms.
Deficiency of ACE2 in Bone-Marrow-Derived Cells Increases Expression of TNF-α in Adipose Stromal Cells and Augments Glucose Intolerance in Obese C57BL/6 Mice

Deficiency of ACE2 in macrophages has been suggested to promote the development of an inflammatory M1 macrophage phenotype. We evaluated effects of ACE2 deficiency in bone-marrow-derived stem cells on adipose inflammation and glucose tolerance in C57BL/6 mice fed a high fat (HF) diet. ACE2 activity was increased in the stromal vascular fraction (SVF) isolated from visceral, but not subcutaneous adipose tissue of HF-fed mice. Deficiency of ACE2 in bone marrow cells significantly increased mRNA abundance of F4/80 and TNF-α in the SVF isolated from visceral adipose tissue of HF-fed chimeric mice, supporting increased presence of inflammatory macrophages in adipose tissue. Moreover, deficiency of ACE2 in bone marrow cells modestly augmented glucose intolerance in HF-fed chimeric mice and increased blood levels of glycosylated hemoglobin. In summary, ACE2 deficiency in bone marrow cells promotes inflammation in adipose tissue and augments obesity-induced glucose intolerance.
Characterization of Bacterial and Fungal Soil Communities by Automated Ribosomal Intergenic Spacer Analysis Fingerprints: Biological and Methodological Variability

ABSTRACT Automated rRNA intergenic spacer analysis (ARISA) was used to characterise bacterial (B-ARISA) and fungal (F-ARISA) communities from different soil types. The 16S-23S intergenic spacer region from the bacterial rRNA operon was amplified from total soil community DNA for B-ARISA. Similarly, the two internal transcribed spacers and the 5.8S rRNA gene (ITS1-5.8S-ITS2) from the fungal rRNA operon were amplified from total soil community DNA for F-ARISA. Universal fluorescence-labeled primers were used for the PCRs, and fragments of between 200 and 1,200 bp were resolved on denaturing polyacrylamide gels by use of an automated sequencer with laser detection. Methodological (DNA extraction and PCR amplification) and biological (inter- and intrasite) variations were evaluated by comparing the number and intensity of peaks (bands) between electrophoregrams (profiles) and by multivariate analysis. Our results showed that ARISA is a high-resolution, highly reproducible technique and is a robust method for discriminating between microbial communities. To evaluate the potential biases in community description provided by ARISA, we also examined databases on length distribution of ribosomal intergenic spacers among bacteria (L. Ranjard, E. Brothier, and S. Nazaret, Appl. Environ. Microbiol. 66:5334–5339, 2000) and fungi.
Effects of bisphosphonates on bone loss in the first year after renal transplantation--a meta-analysis of randomized controlled trials.

BACKGROUND Bone loss remains a serious problem after kidney transplantation and is most pronounced during the first months after engraftment. Bisphosphonates are frequently used to treat post-transplant osteodystrophy, but data of large randomized controlled trials (RCTs) are missing. METHODS We, therefore, conducted this systematic review of the literature, searching electronic databases, reference lists and abstracts from scientific meetings to identify RCTs in all languages. The primary outcome assessed was the change in bone mineral density (BMD) during the early post-transplantation period. Based on the mean BMD change presented in the identified publications, the authors were asked for the individual BMD results of all randomized patients, determined at lumbar spine and femoral neck before and after bisphosphonate therapy. Data were pooled for summary estimates by using weighted mean differences of absolute change in BMD. An analysis of covariance was performed, adjusted for individual baseline values, treatment arm and individual trial. RESULTS Five studies involving 180 participants were included in our meta-analysis. Treatment with bisphosphonates showed a substantial effect in preventing post-transplant osteodystrophy. BMD decline at the lumbar spine within 6-12 months after transplantation was significantly reduced by 0.06 g/cm(2) in patients treated with bisphosphonates (95% CI 0.05-0.08 g/cm(2)). At the femoral neck, the loss of BMD was reduced by 0.05 g/cm(2) during this period (95% CI 0.0-0.11 g/cm(2)), reaching just non-statistical significance. This benefit of bone loss prevention could be reached without major side effects. CONCLUSION Bisphosphonates are effective in preventing bone loss in the early post-transplant period.
Pedestrian navigation system for mobile phones using panoramic landscape images

We have developed a pedestrian navigation system that delivers photorealistic panoramic landscape images using 3D models of a city and related information to mobile phones. In this paper, we define the requirements for smooth mobile phone navigation: low processing load and quick data delivery. To satisfy these requirements, we propose a server-side panoramic image generation mechanism and a divided guidance information transfer technique. This paper presents our proposed mechanism, technique, and developed prototype that achieved smooth pedestrian navigation in experimental results
EyeContext: recognition of high-level contextual cues from human visual behaviour

In this work we present EyeContext, a system to infer high-level contextual cues from human visual behaviour. We conducted a user study to record eye movements of four participants over a full day of their daily life, totalling 42.5 hours of eye movement data. Participants were asked to self-annotate four non-mutually exclusive cues: social (interacting with somebody vs. no interaction), cognitive (concentrated work vs. leisure), physical (physically active vs. not active), and spatial (inside vs. outside a building). We evaluate a proof-of-concept EyeContext system that combines encoding of eye movements into strings and a spectrum string kernel support vector machine (SVM) classifier. Our results demonstrate the large information content available in long-term human visual behaviour and opens up new venues for research on eye-based behavioural monitoring and life logging.
Does the simple dynamical systems approach provide useful information about catchment hydrological functioning in a Mediterranean context? Application to the Ardèche catchment (France)

1) The manuscript presents the implementation of the Kirchner’s methodology for describing a catchment as a “simple dynamical system” in several Mediterranean catchments in France. The implemented methodology is rather new and I support its implementation in different hydrogeological or climatic settings. This would undoubtedly contribute to its further development and identification of the possible limitations such as the ones presented in this paper. In my view, the most important aspect of the paper is the fact that the hydrological data from the operational network (“lower” quality data) has been used in the study. Therefore, the study might presents possible way how the “official” state hydrological monitoring network data could be used for implementing the methodology presented by Kirchner (WRR, 2009). It is known that hydrological model performance generally decreases if there are substantial differences (errors) in the water balance; namely, the water balance presents a basis for most of the hydrological modelling efforts. If the simulation is derived directly from the mass balance (the case of the Kirchner methodology), then the water budget related problems become even more pronounced. The authors have demonstrated that the main limiting factors for the application of the methodology in Mediterranean climatic conditions is limited assessment of the actual evapotranspiration. I believe this should be more clearly pointed out in the paper.
The music effect differentiation in physiological signals

In this paper two types of physiological signals are analyzed from the music effect standpoint. In particular, we considered the state before (b state) and after listening classical music (p state). The signals belonging to each state of silence are analyzed according to the variability of heartbeats. The made correlation between the states describes the music effect. The obtained results seem promising for further discriminative characterization based on physiological signals, such as respiratory and seismocardiogram signals.
Recent advances in the biogeochemistry of nitrogen in the ocean

Until fairly recently, study of the marine nitrogen cycle was considered to be important but a bit dull. Important because nitrogen had long been recognized as an essential nutrient that often limits primary production in the ocean but dull because the residence time of fixed nitrogen in the ocean was believed to be long (∼10 000 yr; Emery et al., 1955), and its budget, like those of most other elements, at or very near steady state. Serious efforts to quantify the key terms in the combined nitrogen budget – denitrification and nitrogen fixation – began in the 1970s, and despite varying estimates provided by different investigators, the notion of a steady state began to be challenged in the mid-1980s (Codispoti and Christensen, 1985, and references therein). The discovery of large glacial-interglacial changes in atmospheric carbon dioxide content based on analyses of polar ice cores (Delmas et al., 1980), arguably one of the most important findings in Earth Sciences in recent years, left paleoclimatologists scrambling for an explanation, and one of the earliest hypotheses offered invoked changes in the fixed nitrogen inventory of the oceans (McElroy, 1983), subsequently refined by Altabet et al. (1995) and Ganeshram et al. (1995). However, the extent to which variations in denitrification or nitrogen fixation can drive changes in nitrogen inventory (Falkowski, 1997) that contribute to climatic cycles, and whether or not the nitrogen budget in today’s ocean is balanced, are issues that remain unsettled (Sigman and Boyle, 2000; Codispoti et al., 2001; Gruber, 2004). The interest in the balance (or lack thereof) between the input and loss terms of the oceanic nitrogen budget has led to a broad range of studies including focused biological measurements of specific processes (e.g., N2-fixation and denitrification), basin-scale geochemical measurements, and integrative modeling (Gruber and Sarmiento, 1997; Brandes et
A re-examination of the predicting power of forward premia

The paper proposes that the spot exchange rate consist of two parts. Important information content is with its underlying movement, in accordance with the development in the economy and the adjustment in economic activity. The paper then extracts the underlying movement from the spot exchange rate using the state space method and the frequency domain method. The extracted component is persistent as expected, catching trend movement and matching the statistical characteristics of the forward premium to some degree. Based on the results, the paper is able to reject the finding in many previous studies that the forward premium predicts the future spot rate in a completely wrong way. The paper concludes that the forward premium does not help explain the future spot rate as its most feasible result.
A Refined Margin Analysis for Boosting Algorithms via Equilibrium Margin

Much attention has been paid to the theoretical explanation of the empirical success of AdaBoost. The most influential work is the margin theory, which is essentially an upper bound for the generalization error of any voting classifier in terms of the margin distribution over the training data. However, important questions were raised about the margin explanation. Breiman (1999) proved a bound in terms of the minimum margin, which is sharper than the margin distribution bound. He argued that the minimum margin would be better in predicting the generalization error. Grove and Schuurmans (1998) developed an algorithm called LP-AdaBoost which maximizes the minimum margin while keeping all other factors the same as AdaBoost. In experiments however, LP-AdaBoost usually performs worse than AdaBoost, putting the margin explanation into serious doubt. In this paper, we make a refined analysis of the margin theory. We prove a bound in terms of a new margin measure called the Equilibrium margin (Emargin). The Emargin bound is uniformly sharper than Breiman's minimum margin bound. Thus our result suggests that the minimum margin may be not crucial for the generalization error. We also show that a large Emargin and a small empirical error at Emargin imply a smaller bound of the generalization error. Experimental results on benchmark data sets demonstrate that AdaBoost usually has a larger Emargin and a smaller test error than LP-AdaBoost, which agrees well with our theory.