Miracle-dz/UniFAR-FTUs huggingface dataset:
Can noise induce chaos

An important component of the mathematical definition of chaos is sensitivity to initial conditions. Sensitivity to initial conditions is usually measured in a deterministic model by the dominant Lyapunov exponent (LE), with chaos indicated by a positive LE. The sensitivity measure has been extended to stochastic models; however, it is possible for the stochastic Lyapunov exponent (SLE) to be positive when the LE of the underlying deterministic model is negative, and vice versa. This occurs because the LE is a long-term average over the deterministic attractor while the SLE is the long-term average over the stationary probability distribution. The property of sensitivity to initial conditions, uniquely associated with chaotic dynamics in deterministic systems, is widespread in stochastic systems because of time spent near repelling invariant sets (such as unstable equilibria and unstable cycles). Such sensitivity is due to a mechanism fundamentally different from deterministic chaos. Positive SLE's should therefore not be viewed as a hallmark of chaos. We develop examples of ecological population models in which contradictory LE and SLE values lead to confusion about whether or not the population fluctuations are primarily the result of chaotic dynamics. We suggest that “chaos” should retain its deterministic definition in light of the origins and spirit of the topic in ecology. While a stochastic system cannot then strictly be chaotic, chaotic dynamics can be revealed in stochastic systems through the strong influence of underlying deterministic chaotic invariant sets.
Investigating the speciation of copper in secondary fly ash by X-ray absorption spectroscopy.

Although some researchers have reported that chlorides may play an important part in the evaporation of copper during heat treatment of municipal solid waste incinerators (MSWI) fly ash (1, 2) , details on the copper speciation in volatile matters (secondary fly ash, SFA) are still lacking. In this work, we used in situ X-ray absorption spectroscopy (XAS) experiments involving three types of SFA, which was collected from a high-temperature tubular electric furnace by thermal treatment of municipal solid waste incinerator (MSWI) fly ash at 1000, 1150, and 1250 degrees C. The results obtained by a linear combination fit (LCF) of X-ray absorption near edge structure (XANES) spectra revealed that in MSWI fly ash copper mainly exists as CuO and CuSO(4). 5H(2)O while chloride almost dominated all the content of the SFA conformation, which was more than 80%. Extended X-ray absorption fine structure (EXAFS) data analysis indicated the presence of both Cu-O and Cu-Cl bonds in the first coordination shell of Cu ions in all SFA, while only Cu-O bonds occur in the MSWI fly ash. Consequently, in the MSWI fly ash during heat treatment copper evaporated as chloride, and the latter plays an important role in the formation of copper chloride.
Memory efficient subsequence DTW for Query-by-Example Spoken Term Detection

In this paper we propose a fast and memory efficient Dynamic Time Warping (MES-DTW) algorithm for the task of Query-by-Example Spoken Term Detection (QbE-STD). The proposed algorithm is based on the subsequence-DTW (S-DTW) algorithm, which allows the search for small spoken queries within a much bigger search collection of spoken documents by considering fixed start-end points in the query and discovering optimal matching subsequences along the search collection. The proposed algorithm applies some modifications to S-DTW that make it better suited for the QbE-STD task, including a way to perform the matching with virtually no system memory, optimal when querying large scale databases. We also describe the system used to perform QbE-STD, including an energy-based quantification for speech/non-speech detection and an overlap detector for putative matches. We test the system proposed using the Mediaeval 2012 spoken-web-search dataset and show that, in addition to the memory savings, the proposed algorithm brings an advantage in terms of matching accuracy (up to 0.235 absolute MTWV increase) and speed (around 25% faster) in comparison to the original S-DTW.
Percolation-Induced Exponential Scaling in the Large Current Tails of Random Resistor Networks

There is a renewed surge in percolation-induced transport properties of diverse nano-particle composites (cf. RSC Nanoscience & Nanotechnology Series, Paul O'Brien Editor-in-Chief). We note in particular a broad interest in nano-composites exhibiting sharp electrical property gains at and above percolation threshold, which motivated us to revisit the classical setting of percolation in random resistor networks but from a multiscale perspective. For each realization of random resistor networks above threshold, we use network graph representations and associated algorithms to identify and restrict to the percolating component, thereby preconditioning the network both in size and accuracy by filtering {\it a priori} zero current-carrying bonds. We then simulate many realizations per bond density and analyze scaling behavior of the complete current distribution supported on the percolating component. We first confirm the celebrated power-law distribution of small currents at the percolation threshold, and second we confirm results on scaling of the maximum current in the network that is associated with the backbone of the percolating cluster. These properties are then placed in context with global features of the current distribution, and in particular the dominant role of the large current tail that is most relevant for material science applications. We identify a robust, exponential large current tail that: 1. persists above threshold; 2. expands broadly over and dominates the current distribution at the expense of the vanishing power law scaling in the small current tail; and 3. by taking second moments, reproduces the experimentally observed power law scaling of bulk conductivity above threshold.
Role of intestinal circadian genes in alcohol-induced gut leakiness.

BACKGROUND Several studies have indicated that endotoxemia is the required co-factor for alcoholic steatohepatitis (ASH) that is seen in only about 30% of alcoholics. Recent studies have shown that gut leakiness that occurs in a subset of alcoholics is the primary cause of endotoxemia in ASH. The reasons for this differential susceptibility are not known. Since disruption of circadian rhythms occurs in some alcoholics and circadian genes control the expression of several genes that are involved in regulation of intestinal permeability, we hypothesized that alcohol induces intestinal hyperpermeability by stimulating expression of circadian clock gene proteins in the intestinal epithelial cells. METHODS We used Caco-2 monolayers grown on culture inserts as an in vitro model of intestinal permeability and performed Western blotting, permeability, and siRNA inhibition studies to examine the role of Clock and Per2 circadian genes in alcohol-induced hyperpermeability. We also measured PER2 protein levels in intestinal mucosa of alcohol-fed rats with intestinal hyperpermeability. RESULTS Alcohol, as low as 0.2%, induced time dependent increases in both Caco-2 cell monolayer permeability and in CLOCK and PER2 proteins. SiRNA specific inhibition of either Clock or Per2 significantly inhibited alcohol-induced monolayer hyperpermeability. Alcohol-fed rats with increased total gut permeability, assessed by urinary sucralose, also had significantly higher levels of PER2 protein in their duodenum and proximal colon than control rats. CONCLUSIONS Our studies: (i) demonstrate a novel mechanism for alcohol-induced intestinal hyperpermeability through stimulation of intestinal circadian clock gene expression, and (ii) provide direct evidence for a central role of circadian genes in regulation of intestinal permeability.
Expression and significance of Musashi-1 in gastric cancer and precancerous lesions.

AIM To investigate expression of stem cell marker Musashi-1 (Msi-1) in relationship to tumorigenesis and progression of intestinal-type gastric cancer (GC). METHODS Endoscopic biopsy specimens and surgical specimens were obtained, including 54 cases of intestinal-type GC, 41 high-grade intraepithelial neoplasia, 57 low-grade intraepithelial neoplasia, 31 intestinal metaplasia, and 36 normal gastric mucosa. Specimens were fixed in 10% paraformaldehyde, conventionally dehydrated, embedded in paraffin, and sliced in 4-μm-thick serial sections. Two-step immunohistochemical staining was used to detect Msi-1 and proliferating cell nuclear antigen (PCNA) expression. Correlation analysis was conducted between Msi-1 and PCNA expression. The relationship between Msi-1 expression and clinicopathological parameters of GC was analyzed statistically. RESULTS There were significant differences in Msi-1 and PCNA expression in different pathological tissues (χ² = 15.37, P < 0.01; χ² = 115.36, P < 0.01). Msi-1 and PCNA-positive cells were restricted to the isthmus of normal gastric glands. Expression levels of Msi-1 and PCNA in intestinal metaplasia were significantly higher than in normal mucosa (U = 392.0, P < 0.05; U = 40.50, P < 0.01), whereas there was no significant difference compared to low or high-grade intraepithelial neoplasia. Msi-1 and PCNA expression in intestinal-type GC was higher than in high-grade intraepithelial neoplasia (U = 798.0, P < 0.05; U = 688.0, P < 0.01). There was a significantly positive correlation between Msi-1 and PCNA expression (r(s) = 0.20, P < 0.01). Msi-1 expression in GC tissues was correlated with their lymph node metastasis and tumor node metastasis stage (χ² = 12.62, P < 0.01; χ² = 11.24, P < 0.05), but not with depth of invasion and the presence of distant metastasis. CONCLUSION Msi-1-positive cells may play a key role in the early events of gastric carcinogenesis and may be involved in invasion and metastasis of GC.
Supportive role played by precore and preS2 genomic changes in the establishment of lamivudine-resistant hepatitis B virus.

BACKGROUND Hepatitis B virus (HBV) establishes lamivudine resistance via the resistance-causative rtM204V/I mutation and the replication-compensatory rtL180M mutation. However, both lamivudine-resistant viruses with and those without rtL180M can exist in clinical settings. To elucidate the differences between viruses with and those without rtL180M, we conducted full-length sequencing analysis of HBV derived from patients with type B chronic hepatitis showing lamivudine resistance. METHODS The full-length HBV DNA sequences derived from 44 patients showing lamivudine resistance were determined by polymerase chain reaction direct sequencing. Viral replicative competence was examined by in vitro transfection analysis using various HBV-expressing plasmids. RESULTS Throughout the HBV genome, a precore-defective A1896 mutation and a short deletion in the preS2 gene were detected more frequently in viruses without rtL180M than in those with it (64% vs. 17% [P < .005] and 50% vs. 10% [P < .01], respectively). In vitro transfection analysis revealed that the level of reduction in intracellular viral replication caused by the introduction of lamivudine resistance-associated mutations was lower in precore-defective and preS2-deleted viruses than in wild-type virus. CONCLUSIONS Both the precore-defective mutation and the preS2 deletion may play a supportive role in the replication of lamivudine-resistant HBV, which may be a reason for there being no need for the compensatory rtL180M mutation in lamivudine-resistant HBV possessing the precore and preS2 genomic changes.
Vinflunine treatment in patients with metastatic urothelial cancer: A Nordic retrospective multicenter analysis

In 2009, vinflunine was introduced as a second-line treatment to be used after the failure of platinum therapy in patients with metastatic urothelial carcinoma (mUC). The present study investigated the administered vinflunine to patients with mUC in standard clinical practice with the aim of evaluating treatment patterns, response, survival parameters and side-effects. Data were collected retrospectively from the first 100 mUC patients treated with vinflunine at three Nordic cancer centers associated with the Nordic Urothelial Cancer Oncology Group. The overall response rate was 23% and complete response was observed in one patient. The median progression-free survival (mPFS) and median overall survival (mOS) were 2.8 (range, 0.5–34.3) and 6.3 (range, 0.3–39.7) months, respectively. An Eastern Cooperative Oncology Group performance status (ECOG PS) of 2 was present in 20% of the patients, and those patients exhibited significantly shorter mOS (4.1 vs. 7.0 months, P=0.001) and a significantly higher degree of grade 3/4 toxicity (P=0.026) compared with ECOG PS 0–1 patients. Furthermore, patients without visceral metastases had significantly longer mOS than patients with visceral metastases (10.6 vs. 6.0 months, P=0.008). The median number of cycles of vinflunine was 3 (range, 1–28). The current data confirms that vinflunine is an active agent for second-line treatment in an unselected clinical cohort of patients with mUC. ECOG PS and presence of visceral metastases were significant prognostic parameters. In particular, patients with ECOG PS 2 receiving vinflunine had a shorter mOS and a higher frequency of severe toxicity, and, thus, should be treated with caution. Furthermore, the present study observed large inter-individual differences in radiological response and OS, indicating the need for further development of improved patient selection tools to optimize vinflunine treatment in platinum-refractory mUC patients.
Stereoscopic Datasets and Algorithm Evaluation for Driving Scenarios

This report presents novel binocular stereo video datasets that capture automotive driving relevant scenarios as well as evaluation of five disparity estimation algorithms on the acquired imagery. Binocular stereo has great potential as a component technology for driving assistance, as it provides an approach to recovering 3D distance relative to a vehicle and thereby provide critical information for a variety of driving tasks. For incorporation into an overall driving system, candidate algorithms must have their performance specified precisely. The acquired imagery and comparative algorithm evaluation respond to this need by providing detailed qualitative and quantitative evaluation of alternative disparity estimation approaches on driving relevant data. Chapter
The Activation of M1 Muscarinic Receptor Signaling Induces Neuronal Differentiation in Pyramidal Hippocampal Neurons

Muscarinic receptors have been proposed to play an important role during brain development by regulating cell survival, proliferation, and differentiation. This study investigated the effect of muscarinic receptor activation on prenatal rat hippocampal pyramidal neuron differentiation and the signal transduction pathways involved in this effect. The cholinergic agonist carbachol, after 24 h in vitro, increased the length of the axon, without affecting the length of minor neurites. Carbachol-induced axonal growth was also observed in pyramidal neurons from the neocortex but not in granule neurons from the cerebellum. The effect of carbachol was mediated by the M1 subtype of muscarinic receptors. The Ca2+ chelator 1,2-bis(2-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid-acetoxymethyl ester, the two protein kinase C (PKC) inhibitors 3-[1-[3-(dimethylaminopropyl]-1H-indol-3-yl]-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione monohydrochloride (GF109203X) and 2-{8-[(dimethylamino)methyl]-6,7,8,9-tetrahydropyridol[1,2-a]indol-3-yl}-3-(1-methylindol-3-yl)maleimide (Ro-32-0432), and the extracellular signal-regulated kinase (ERK)1/2 inhibitors 2′-amino-3′-methoxyflavone (PD98059) and 1,4-diamino-2,3-dicyano-1,4-bis(methylthio)butadiene (U0126) all blocked carbachol-induced axonal outgrowth. In addition, down-regulation of ERK1/2 with small interfering RNA abolished the neuritogenic effect of carbachol. These data suggest an involvement of Ca2+, PKC, and ERK1/2 in carbachol-induced axonal growth. Carbachol indeed increased the release of Ca2+ from intracellular stores and induced PKC and ERK1/2 activation. Additional experiments showed that PKC, but not Ca2+, is involved in carbachol-induced ERK1/2 activation. Together, these results show that cholinergic stimulation of prenatal hippocampal pyramidal neurons accelerates axonal growth through the induction of Ca2+ mobilization and the activation of PKC and especially of ERK1/2.
Effects of rainfall variation on rice production in the Ganges-Brahmaputra Basin

Rice production in India is highly correlated with monsoon rainfall. The relationships between rainfall variation and rice production have attracted significant interest at a country scale in Asia, but regional differences within a country remain unclear. In this study, we examined the effects of rainfall variation on 'kharif' rice (rainy season rice)—including temporal changes in this relation- ship—in the Ganges-Brahmaputra Basin, using a statistical model and a district-level data series of rice production and rainfall. Three homogeneous regions were identified within the study area. In the upper Ganges, the drought effect on rice production was dominant; however it became less pro- nounced due to decreased rainfall variation. In the lower Ganges, the flood effect increased due to increased rainfall. In the Brahmaputra Basin, the drought effect increased due to increased rainfall variation. Non-stationarity in the rainfall-rice production relationship was caused mainly by changes in rainfall patterns; however the impact of other factors, including social factors, should be evaluated on a regional scale.
Deep learning, audio adversaries, and music content analysis

We present the concept of adversarial audio in the context of deep neural networks (DNNs) for music content analysis. An adversary is an algorithm that makes minor perturbations to an input that cause major repercussions to the system response. In particular, we design an adversary for a DNN that takes as input short-time spectral magnitudes of recorded music and outputs a high-level music descriptor. We demonstrate how this adversary can make the DNN behave in any way with only extremely minor changes to the music recording signal. We show that the adversary cannot be neutralised by a simple filtering of the input. Finally, we discuss adversaries in the broader context of the evaluation of music content analysis systems.
Prevalence of High-Risk Human Papillomavirus in Women With Abnormal and Normal Vaginal ThinPrep Papanicolaou Cytology

Objective. The significance of high-risk HPV (hrHPV) testing in the management of women with abnormal cervical Pap tests is well known. However, the data about the hrHPV detection and its significance in abnormal vaginal specimens are very limited. The purpose of this study was to assess the prevalence of hrHPV in women with abnormal vaginal smears. Methods. Our Copath database system was searched to retrieve all the vaginal Pap tests with adjunctive HC2 hrHPV DNA test performed between July 1, 2005, and July 30, 2009. The results of hrHPV were reviewed in different TBS 2001 categories, in different age groups, and in white and African American women. Results. During the study period, there were 1,320 vaginal ThinPrep Pap tests with adjunctive HC2 hrHPV, reported as atypical squamous cells of undetermined significance (n = 1,125), atypical squamous cells cannot rule out high grade (n = 36), low-grade squamous intraepithelial lesion (n = 148), and high-grade squamous intraepithelial lesion (n = 11). A positive hrHPV DNA result was obtained in a total of 387 cases (29.3%), which included 244 atypical squamous cells of undetermined significance (21.7%), 21 atypical squamous cells cannot rule out high-grade (58.3%), 113 low-grade squamous intraepithelial lesion (76.4%), and 9 high-grade squamous intraepithelial lesions (81.8%). Mean age was 56.5 years (range = 17-93 y). High-risk HPV-positive rate was 34.5% versus 24.9% in women aged 54 years or younger compared with those aged ≥55 years or older (p < .001) and 45.1% versus 27.3% in African American women compared with white women (p < .001). High-risk HPV DNA-positive rate was 2.6% among the 1,572 women with negative vaginal Pap tests. Conclusions. Our results show that prevalence of hrHPV in abnormal vaginal smears parallels that of cervical smears with equivalent degree of abnormality. The suggestion of reflex hrHPV testing as a tool in formulating the management plan for women with abnormal vaginal smears needs further attention.
Commentary: Models of Sleep Regulation: Successes and Continuing Challenges

Quantitative models have been developed to describe salient aspects of human sleep regulation. The two-process model of sleep regulation and the thermoregulatory model of sleep control highlight the interaction between sleep homeostasis and circadian rhythmicity and the association between sleep and temperature regulation, respectively. These models have been successful and inspiring, but continuing progress remains dependent on rigorous testing of some of their basic assumptions. Whereas it has been established that EEG slowwave activity is a marker of sleep homeostasis, its causal role in regulating the timing of sleep and wakefulness remains to be demonstrated conclusively. Likewise, the causal role of the temperature regulatory system in sleep timing requires further investigation. In both models, many parameters have yet to be associated with specific physiologic processes. This makes it challenging, at least within the framework of these models, to account for interindividual differences or age-related changes in such features as sleep duration and sleep timing, as well as changes in the phase angle between the sleep-wake cycle and accepted markers of the circadian pacemaker, such as the body temperature or melatonin rhythm. Although the models may describe adequately global sleep patterns and their circadian modulation, detailed modeling of the frequent short awakenings from, and the subsequent transitions back to, sleep, as well as the variation of the propensity to awaken across the ultradian non-REM-REM cycle, is not addressed. Incoporation of these aspects of sleep in mathematical models of sleep regulation may further our understanding of a key aspect of sleep regulation, that is, its timing.