Miracle-dz/UniFAR-FTUs huggingface dataset:
Sound-induced synchronization of neural activity between and within three auditory cortical areas.

Neural synchrony within and between auditory cortical fields is evaluated with respect to its potential role in feature binding and in the coding of tone and noise sound pressure level. Simultaneous recordings were made in 24 cats with either two electrodes in primary auditory cortex (AI) and one in anterior auditory field (AAF) or one electrode each in AI, AAF, and secondary auditory cortex. Cross-correlograms (CCHs) for 1-ms binwidth were calculated for tone pips, noise bursts, and silence (i.e., poststimulus) as a function of intensity level. Across stimuli and intensity levels the total percentage of significant stimulus onset CCHs was 62% and that of significant poststimulus CCHs was 58% of 1,868 pairs calculated for each condition. The cross-correlation coefficient to stimulus onsets was higher for single-electrode pairs than for dual-electrode pairs and higher for noise bursts compared with tone pips. The onset correlation for single-electrode pairs was only marginally larger than the poststimulus correlation. For pairs from electrodes across area boundaries, the onset correlations were a factor 3-4 higher than the poststimulus correlations. The within-AI dual-electrode peak correlation was higher than that across areas, especially for spontaneous conditions. Correlation strengths for between area pairs were independent of the difference in characteristic frequency (CF), thereby providing a mechanism of feature binding for broadband sounds. For noise-burst stimulation, the onset correlation for between area pairs was independent of stimulus intensity regardless the difference in CF. In contrast, for tone-pip stimulation a significant dependence on intensity level of the peak correlation strength was found for pairs involving AI and/or AAF with CF difference less than one octave. Across all areas, driven rate, between-area peak correlation strength, or a combination of the two did not predict stimulus intensity. However, between-area peak correlation strength performs better than firing rate to decide if a stimulus is present or absent.
Homocysteine, folate, vitamin B12, and cardiovascular risk in Indians, Malays, and Chinese in Singapore

OBJECTIVE To examine the hypothesis that the higher rates of coronary heart disease (CHD) in Indians (South Asians) compared with Malays and Chinese is partly attributable to differences in blood concentrations of homocysteine, and related blood concentrations of folate and vitamin B12. DESIGN Cross sectional study of the general population. SETTING Singapore. PARTICIPANTS Random sample of 726 fasting subjects aged 30 to 69 years. MAIN RESULTS Mean plasma total homocysteine concentrations did not show significant ethnic differences; values were Indians (men 16.2 and women 11.5 μmol/l), Malays (men 15.0 and women 12.5 μmol/l), and Chinese (men 15.3 and women 12.2 μmol/l). Similarly, the proportions with high plasma homocysteine (>14.0 μmol/l) showed no important ethnic differences being, Indians (men 60.0 and women 21.9 %), Malays (men 53.9 and women 37.8 %), and Chinese (men 56.6 and women 30.6 %). Mean plasma folate concentrations were lower in Indians (men 8.7 and women 10.9 nmol/l) and Malays (men 8.5 and women 10.8 nmol/l), than Chinese (men 9.7 and women 13.8 nmol/l). Similarly, the proportions with low plasma folate (<6.8 nmol/l) were higher in Indians (men 44.9 and women 36.6 %) and Malays (men 45.3 and women 24.5 %) than Chinese (men 31.4 and women 12.6 %). Mean plasma vitamin B12 concentrations were lowest in Indians (men 352.5 and women 350.7 pmol/l), then Chinese (men 371.1 and women 373.7 pmol/l), and then Malays (men 430.5 and women 486.0 pmol/l). CONCLUSION While there were ethnic differences for plasma folate and vitamin B12 (in particular lower levels in Indians), there was no evidence that homocysteine plays any part in the differential ethnic risk from CHD in Singapore and in particular the increased susceptibility of Indians to the disease.
Dendrosomatic Sonic Hedgehog Signaling in Hippocampal Neurons Regulates Axon Elongation

The presence of Sonic Hedgehog (Shh) and its signaling components in the neurons of the hippocampus raises a question about what role the Shh signaling pathway may play in these neurons. We show here that activation of the Shh signaling pathway stimulates axon elongation in rat hippocampal neurons. This Shh-induced effect depends on the pathway transducer Smoothened (Smo) and the transcription factor Gli1. The axon itself does not respond directly to Shh; instead, the Shh signal transduction originates from the somatodendritic region of the neurons and occurs in neurons with and without detectable primary cilia. Upon Shh stimulation, Smo localization to dendrites increases significantly. Shh pathway activation results in increased levels of profilin1 (Pfn1), an actin-binding protein. Mutations in Pfn1's actin-binding sites or reduction of Pfn1 eliminate the Shh-induced axon elongation. These findings indicate that Shh can regulate axon growth, which may be critical for development of hippocampal neurons. SIGNIFICANCE STATEMENT Although numerous signaling mechanisms have been identified that act directly on axons to regulate their outgrowth, it is not known whether signals transduced in dendrites may also affect axon outgrowth. We describe here a transcellular signaling pathway in embryonic hippocampal neurons in which activation of Sonic Hedgehog (Shh) receptors in dendrites stimulates axon growth. The pathway involves the dendritic-membrane-associated Shh signal transducer Smoothened (Smo) and the transcription factor Gli, which induces the expression of the gene encoding the actin-binding protein profilin 1. Our findings suggest scenarios in which stimulation of Shh in dendrites results in accelerated outgrowth of the axon, which therefore reaches its presumptive postsynaptic target cell more quickly. By this mechanism, Shh may play critical roles in the development of hippocampal neuronal circuits.
Accounts, excuses, and apologies : a theory of image restoration strategies

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Echocardiographically Derived Parameters of Fluid Responsiveness

The prediction of fluid responsiveness during resuscitation has become an increasingly studied topic over the last several years. Optimizing hemodynamics is the foundation of managing the critically ill patients in the operating room and in the intensive care unit (ICU). This is especially true as perioperative preload augmentation with fluid bolus administration is a quick method to improve cardiac output (CO) and therefore hemodynamics. However, unnecessary fluid administration can lead to the development of pulmonary edema and increase the risk of acute respiratory distress syndrome, resulting in increased morbidity and mortality. As a result, it is of utmost importance to determine accurate parameters to guide fluid therapy and hemodynamic optimization, while avoiding administration of ineffective and possibly harmful therapy. It has been reported that only 40% to 72% of critically ill patients will respond to volume expansion by a significant increase
Computation and Graphical Characterization of Robust Multiple-Contact Postures in 2D Gravitational Environments

This paper is concerned with the problem of identifying robust equilibrium postures of a planar mechanism supported by fixed frictional contacts in a two-dimensional gravitational field. The complex kinematic structure of the mechanism is lumped into a single rigid body, B, with a variable center of mass. Inertial forces generated by moving parts of the mechanism are lumped into a neighborhood of wrenches centered at the nominal gravitational wrench. The identification of the robust equilibrium postures associated with a given set of contacts is reduced to the identification of center-of-mass locations that maintain equilibrium of B with respect to any wrench in the given neighborhood. The static response of B to an external wrench involves static indeterminacy and frictional constraints. The region of center-of-mass locations that generate equilibrium with respect to a particular external wrench is formulated as a linear programming problem, and a full graphical characterization is provided. The result is then generalized to robust equilibrium postures that resist a neighborhood of external wrenches. Finally, we present experimental results that validate the criteria for feasible equilibrium postures.
End-to-End Deep Neural Network for Automatic Speech Recognition

We investigate the efficacy of deep neural networks on speech recognition. Specifically, we implement an end-to-end deep learning system that utilizes mel-filter bank features to directly output to spoken phonemes without the need of a traditional Hidden Markov Model for decoding. The system will comprise of two variants of neural networks for phoneme recognition. In particular, we utilize convolutional for frame level classification and recurrent architecture with Connectionist Temporal Classification loss for decoding the frames into a sequence of phonemes. We carry out our experiments on the TIMIT dataset. We have managed to obtain 22.1% for the frame error rate with our CNN, which to our knowledge, closely matches the state-of-the-art. Our decoded phone sequence achieves an error of 29.4%.
A time-dependent SIS-model for long-term computer worm evolution

Epidemic models like the SIS or SIR model enable us to describe simple spreading processes over networks but are often not sufficient to accurately capture more complex network dynamics as exhibited by sophisticated and malicious computer worms. Many of the common assumptions behind epidemic models do not necessary hold if the process under investigation spans big networks or large scales of time. We extend the standard SIS network model by dropping the assumption of a constant curing rate in favour of a time-dependent curing rate function, which enables us to reflect changes in the effectiveness of the active worm removal process over time. The resulting time-dependent mean-field SIS model allows us to study the evolution of the size of computer worm bot-nets. We exemplify the complete procedure, including data-processing, needed to obtain a reliable model on data from Conficker, an extremely resilient computer worm. Using empirical data obtained from the Conficker sinkhole, we fit long time periods of up to 6 years on multiple scales and different levels of noise. We end by reflecting on the limits of epidemic models in empirical analysis of malware threats.
Measures of Autonomic Nervous System Regulation

Abstract : Mind-body health practices aim to regulate activation of the sympathetic nervous system (SNS) to maintain homeostasis within the autonomic nervous system (ANS). The activation of the SNS is directly related to stress response, which, if persistent or prolonged, may lead to physiological and psychological damage. The ability to return to homeostasis after exposure to a stressor or to moderate SNS activation is a measure of resilience. In order to measure the effects of mind-body skills in facilitating resilience, tools may be used that are sensitive to the changes in activation and allow for feedback to guide practice. The most promising and most often used measures of ANS activation encompass non-invasive tools, which measure cardiac, skin conductance, respiratory, and vascular activity. Choice of tools is dependent upon a variety of factors, including setting, purpose, user friendliness and psychometric properties. In this companion paper to Mind-body Skills for Regulating the Autonomic Nervous System, a brief overview of ANS activity, as well as a review of the physiological measurement of stress, is presented. A description of tools which measure the nine ANS pathways is also presented. Finally, a decision tree is offered to aid in choosing appropriate tools for measurement of the effects of mind-body skills.
Adapting learning techniques for visual recognition

Adapting Learning Techniques for Visual Recognition by Hao Zhang Doctor of Philosophy in Computer Science University of California, Berkeley Professor Jitendra Malik, Chair This thesis builds on previous work on shape matching techniques in computer vision, and classification techniques in machine learning. It tries to model the visual recognition task as one based on comparison to prototypes. Careful attention is paid to insights from perception and neuroscience on the nature of human visual similarity. Classifying hand written digits has been heavily researched, and serves as a clearlydefined shape matching problem. One contribution of this thesis is a prototype-based classifier that drastically reduces the number of prototypes needed for the nearest neighbor technique. A second contribution of this thesis is a technique for determining what parts of the shape are most informative for classification. This notion can be formalized in the framework of “feature selection” as in machine learning. The study of discriminative power from feature selection yields insight on (1) the usefulness of individual parts of the shape (2) the classification process of a general linear model classifier on shape data. The most significant contribution of this thesis is a new learning technique for visual categorization, “SVM-KNN” , which draws on aspects of two well known techniques: support vector machines (SVM) and K-nearest neighbor. The basic idea is to
Enhanced Functionality of CD4+CD25highFoxP3+ Regulatory T Cells in the Peripheral Blood of Patients with Prostate Cancer

Purpose: CD4+CD25highFoxP3+ regulatory T cells (Treg) have been shown to inhibit the activation and function of T cells that participate in antigen-specific immune responses. Higher levels of Tregs have been reported in the peripheral blood of patients with several types of tumors. In this study, we investigated the number and functionality of CD4+CD25highFoxP3+ Tregs in patients with prostate cancer (PCa), and their potential role in inhibiting antitumor immune responses. Experimental Design: Levels of Tregs in the peripheral blood of healthy donors and patients with biochemically progressive, localized, and metastatic PCa were each measured by flow cytometry. The functional activity of Tregs was determined by their ability to suppress the proliferation of CD4+CD25− T cells. Data were analyzed using Wilcoxon rank sum test and unpaired Student's t test. Results: Although levels of Tregs in the peripheral blood of patients with PCa were not significantly higher than those in healthy donors, Tregs in patients with PCa had significantly greater suppressive functionality than Tregs from healthy donors (P < 0.05). Additionally, there was a direct correlation between the serum levels of prostaglandin E2 and Treg functionality in patients with localized PCa, using Pearson's product-moment correlation coefficient (R). Conclusions: These findings further show the potential importance of Tregs in modifying immune responses in patients with PCa. Although longer studies are necessary to confirm these findings, these studies also show for the first time the differences in Treg populations in patients with various stages of PCa, and thus, provide a basis for determining which PCa patient populations are best suited for immunotherapy trials involving the inhibition of Tregs.
Enterotoxigenic Clostridium perfringens: Detection and Identification

Recent advances in understanding the genetics of enterotoxigenic Clostridium perfringens, including whole genome sequencing of a chromosomal cpe strain and sequencing of several cpe-carrying large plasmids, have led to the development of molecular approaches to more precisely investigate isolates involved in human gastrointestinal diseases and isolates present in the environment. Sequence-based PCR genotyping of the cpe locus (cpe genotyping PCR assays) has provided new information about cpe-positive type A C. perfringens including: 1) Foodborne C. perfringens outbreaks can be caused not only by chromosomal cpe type A strains with extremely heat-resistant spores, but also less commonly by less heat-resistant spore-forming plasmid cpe type A strains; 2) Both chromosomal cpe and plasmid cpe C. perfringens type A strains can be found in retail foods, healthy human feces and the environment, such as in sewage; 3) Most environmental cpe-positive C. perfringens type A strains carry their cpe gene on plasmids. Moreover, recent studies indicated that the cpe loci of type C, D, and E strains differ from the cpe loci of type A strains and from the cpe loci of each other, indicating that the cpe loci of C. perfringens have remarkable diversity. Multi-locus sequence typing (MLST) indicated that the chromosomal cpe strains responsible for most food poisoning cases have distinct genetic characteristics that provide unique biological properties, such as the formation of highly heat-resistant spores. These and future advances should help elucidate the epidemiology of enterotoxigenic C. perfringens and also contribute to the prevention of C. perfringens food poisoning outbreaks and other CPE-associated human diseases.
An improvement of steganography scheme based on complete complementary codes

Information hiding scheme using direct sequence spread spectrum (DS-SS) technique is one of the effective ways to embed secret information into media contents securely. In recent years, information hiding schemes based on complete complementary codes have been proposed. In particular, it has been shown that it is possible to embed a large message into an image by a blind steganography scheme based on complete complementary codes. However, it has been pointed out that bit errors occur since the source image is not referred to by the blind scheme. In this paper, we apply low-density parity-check (LDPC) codes to the steganography scheme and analyze the bit error rate (BER) performance by numerical experiments.
Combinatorial Motion Planning Algorithms for a Heterogeneous Collection of Unmanned Vehicles

Abstract : The project dealt with two classes of core decision-making algorithms related to operator-UV collaboration; the first class involves the routing of UVs through the set of targets nominated by the operator and the second class of problems involves decision-making algorithms for UVs to accommodate uncertainty. We have developed approximation, lower bounding and exact algorithms to address the two classes of problems. We have also implemented these algorithms in simulations to corroborate the performance of these algorithms. In the ensuing discussion, we will summarize our work for the project, and our main results.
Regulation of ENaC‐mediated sodium transport by glucocorticoids in Reissner's membrane epithelium

Reissner's membrane (RM) epithelium forms much of the barrier that sustains the large ionic differences between cochlear endolymph and perilymph. We reported that RM contributes to normal cochlear function by absorption of Na from endolymph via the epithelial sodium channel (ENaC) in gerbil inner ear [Lee et al, Neuroscience, 2003].
SC1/Hevin and Reactive Gliosis After Transient Ischemic Stroke in Young and Aged Rats

SC1 is a member of the SPARC family of glycoproteins that regulate cell-matrix interactions in the developing brain. SC1 is expressed in astrocytes, but nothing is known about the expression in the aged or after stroke. We found that after focal striatal ischemic infarction in adult rats, SC1 increased in astrocytes surrounding the infarct and in the glial scar, but in aged rats, SC1 was lower at the lesion edge. Glial fibrillary acidic protein (GFAP) also increased, but it was less prominent in reactive astrocytes further from the lesion in the aged rats. On the basis of their differential expression of several molecules, 2 types of reactive astrocytes with differing spatiotemporal distributions were identified. On Days 3 and 7, SC1 was prevalent in cells expressing markers of classic reactive astrocytes (GFAP, vimentin, nestin, S100&bgr;), as well as apoliprotein E (ApoE), interleukin 1&bgr;, aggrecanase 1 (ADAMTS4), and heat shock protein 25 (Hsp25). Adjacent to the lesion on Days 1 and 3, astrocytes with low GFAP levels and a "starburst" SC1 pattern expressed S100&bgr;, ApoE, and Hsp32 but not vimentin, nestin, interleukin 1&bgr;, ADAMTS4, or Hsp25. Neither cell type was immunoreactive for NG2,CC-1, CD11b, or ionized calcium-binding adapter-1. Their differing expression of inflammation-related and putatively protective molecules suggests different roles for starburst and classic reactive astrocytes in the early glial responses to ischemia.
Women’s reflections about their past abortions

Previous studies have argued that women’s responses to abortion are similar to a linear grief reaction. The present study aimed to explore how women reflect upon their past abortions in the longer term. Interpretative Phenomenological Analysis was used to analyse the transcripts of ten interviews with women who had had an abortion between one and nine years previously. The results showed that although a few women reported a linear pattern of change in their emotions, many also described different patterns including persistent upset that remained ongoing many years after the event, negative reappraisal some time after the event and a positive appraisal at the time of the event with no subsequent negative emotions. The results also provide some insights into this variability. Those who described how they had never been upset or experienced a linear recovery also tended to conceptualise the foetus as less human, reported having had more social support and described either a belief that abortions are supported by society or an ability to defend against a belief that society is judgemental. In contrast patterns of emotional change involving persistent upset or negative appraisal were entwined with a more human view of the foetus, a lack of social support and a belief that society is either overly judgemental or negates the impact that an abortion can have on a woman. To conclude, women’s responses to their abortion do not always follow the suggested reactions of grief but are varied and located within both the personal and social context.