Miracle-dz/UniFAR-FTUs huggingface dataset:
Overview of cell death signaling pathways

Apoptosis plays an important role in development and maintenance of tissue homeostasis. Intensive efforts have been made to explore the molecular mechanisms of the apoptotic signaling pathways including the initiation, mediation, execution, and regulation of apoptosis. Caspases are central effectors of apoptosis. Cells undergo apoptosis through two major pathways, namely the extrinsic pathway (death receptor pathway) or the intrinsic pathway (the mitochondrial pathway). Finally, the contents of dead cells are packaged into apoptotic bodies, which are recognized by neighboring cells or macrophages and cleared by phagocytosis. Cellular apoptosis is tightly controlled by complex regulatory networks including balancing pro-survival signals. De-regulation of apoptosis may lead to pathological disorders such as developmental defects, autoimmune diseases, neurodegeneration or cancer. Increasing attention is being focused on alternative signaling pathways leading to cell death including necrosis, autophagy, and mitotic catastrophe. Understanding of cell death signaling pathways is relevant to understanding cancer and to developing more effective therapeutics.
DiffTools: Electron diffraction software tools for DigitalMicrograph™

A suite of software tools (DiffTools) has been developed for DigitalMicrograph—a software platform widely used in transmission electron microscopy (TEM) laboratories world‐wide. These tools include capabilities for calibration, center determination, rotational averaging with automatic peak location, pattern spot spacing and interspot angle determination, rotation and inset of a pattern into an image, pattern intensity inversion and enhancement, and calculation of basic crystallographic data. The implementation and application of these tools to experimental diffraction patterns is illustrated and measurement of d‐spacings with an accuracy of 0.63% or better is demonstrated. These tools, which are freely available via the Internet, enable users to rapidly and efficiently process selected area electron diffraction patterns. This can be performed entirely within the DigitalMicrograph environment using familiar menu‐based commands and user‐friendly dialog‐based scripts. Microsc. Res. Tech., 2008. © 2008 Wiley‐Liss, Inc.
Differences between diurnal patterns of salivary cortisol and dehydroepiandrosterone in healthy female adolescents

The adrenal hormones cortisol and dehydroepiandrosterone (DHEA) share a common secretagogue: adrenocorticotropic hormone; however, secretion of these hormones can be dissociated suggesting subtle individual regulation at the level of the adrenal gland. We examined differences in the diurnal patterns of cortisol and DHEA secretion in healthy adolescent girls, with the aim of informing the possibility of exploiting these differences to aid interpretation of data from clinical populations in which these patterns can become dysregulated. Fifty-six healthy females aged 10–18 years provided saliva samples at 0 and 30 min (morning samples) and 12 h post-awakening on 2 consecutive weekdays. For morning salivary cortisol in relation to morning DHEA concentrations, correlational analysis revealed only a trend (p = 0.054). Similarly, the association between evening cortisol and DHEA was characterised as a trend (p = 0.084). Mean morning DHEA concentrations showed more day-to-day consistency than equivalent cortisol samples (r = 0.829 for DHEA and 0.468 for cortisol; z = 3.487, p < 0.0005). Unlike the cortisol pattern, characterised by a marked awakening response (cortisol awakening response, CAR), a significant rise in DHEA concentration post-awakening was not evident. Finally, there was a strong association between morning and evening concentrations of DHEA, not found for cortisol. The study shows differences in cortisol and DHEA secretion in the post-awakening period and informs work that seeks to examine correlates of dysregulated hypothalamic–pituitary–adrenal axis function. Parallel examination of both hormones enables enhanced interpretation of aberrant patterns of the CAR, i.e. an exploration of whether dysregulation affects both hormones (reflecting overall steroidogenic capacity) or cortisol alone (CAR-specific mechanisms).
Real time distributed control systems using RTAI

The paper outlines the design and implementation of the Real Time Application Interface (RTAI) for Linux, as used for high performance local/distributed control systems implemented on low cost off the shelf general purpose computers. Its native lean real time middleware layer is described along with its use in an advanced tool to easily manage and monitor complex networked control systems.
Extended Park's transformation for 2/spl times/3-phase synchronous machine and converter phasor model with representation of AC harmonics

A model of the 2/spl times/3-phase synchronous machine is presented using a new transformation based on the eigenvectors of the stator inductance matrix. The transformation fully decouples the stator inductance matrix, and this leads to an equivalent diagram of the machine with no mutual couplings in the stator. A consistent method is developed to determine model parameters from standard machine data. A phasor model of the line commutated converter is presented. The converter model includes not only the fundamental frequency, but also any chosen number of harmonics without a representation of the single thyristors. >
Complement activation in sudden deafness.

OBJECTIVE To test whether complement activation is associated with sudden deafness. DESIGN Plasma samples obtained from patients in the acute phase of sudden deafness were analyzed for complement activation measured by C3bc levels and terminal complement complex. Comparisons were made with plasma samples from healthy controls. PATIENTS Twenty-five adult patients with unilateral sudden deafness. The criteria for inclusion were symptoms of hearing loss for not longer than 14 days and a hearing loss of 35 dB or more measured at entry. RESULTS Levels of C3bc were higher in patients compared with controls (P<.001). There were no differences in the formation of terminal complement complex in patients and controls. CONCLUSIONS The elevated levels of C3bc in patients with sudden deafness indicate an activation of the first part of the complement cascade and therefore suspected inflammatory causes. Measurements of C3bc levels might identify patients with sudden deafness who would benefit from treatment with anti-inflammatory drugs.
Evolving Real-time Heuristic Search Algorithms

Heuristic search is a core area of Artificial Intelligence, successfully applied to planning, constraint satisfaction and game playing. In real-time heuristic search autonomous agents interleave planning and plan execution and access environment locally which make them more suitable for Artificial Life style settings. Over the last two decades a large number of real-time heuristic search algorithms have been manually crafted and evaluated. In this paper we break down several published algorithms into building blocks and then let a simulated evolution re-combine the blocks in a performance-based way. Remarkably, even relatively short evolution runs result in algorithms with state-of-the-art performance. These promising preliminary results open exciting possibilities in the field of real-time heuristic search.
Soft-output MMSE V-BLAST detector under ML channel estimation and channel correlation

Channel estimation errors have not been taken into account by existing soft-output minimum mean square error (MMSE) vertical Bell Lab Space Time (V-BLAST) detectors. As a result, the system performance will be degraded under practical channel estimation. In this letter, we propose a novel soft-output MMSE V-BLAST detector, which takes the estimation error of maximum likelihood (ML) multiple-input multiple-output (MIMO) channel estimation and receiver spatially correlation into account in the computation of the MMSE filter and log likelihood ratio (LLR) of each coded bit. When compared with existing MMSE V-BLAST detectors, simulation results show that the proposed novel detector can obtain sizable performance gain.
Fatty acid composition of Oncorhynchus mykiss during embryogenesis and other developmental stages

Fatty acid compositions of rainbow trout Oncorhynchus mykiss (Walbaum, 1792) was determined during embryogenesis, yolk-sac fry, swim up fry and fry stages. Embryonic and yolk-sac development of fertilized eggs were followed until fry weighed 25 g and samples were taken from each stage to analyse fatty acid composition. Analyses of fatty acid composition were performed by gas chromatography mass spectrometry. Throughout all the developmental stages of O. mykiss important changes, such as an increase in the percentage of 18:2, 18:3 and 20:5 and as a decrease in the percentage of 14:0, 16:2, 20:0, 20:2, 20:3, 20:4 and 22:0 were observed in the amounts of fatty acid of developing eggs. During transition from the embryonic to the yolk-sac stage, an important increase in 20:0, 20:3, 20:5, 22:0 and a decrease in 18:3, 22:1 was determined between 45-day old embryo and yolk-sac fry. During transition from the 43 day yolk-sac stage to swim up stage, a decrease in the percentage of 18:0, 20:2 and an increase in the percentage of 14:0, 16:2, 18:2, 18:3 was seen. In all the observed stages, no qualitative but significant quantitative variations were determined in the fatty acid composition of O. mykiss. It may be concluded that 14:0, 16:0, 16:1, 18:0, 18:1 18, 20 and 22 polyunsaturated fatty acids are necessary for normal development of O. mykiss during their life stages.
Contribution of defects in glucose uptake to carbohydrate intolerance in liver cirrhosis: assessment during physiological glucose and insulin concentrations.

It is well established that subjects with liver cirrhosis are insulin resistant, but the contribution of defects in insulin secretion and/or action to glucose intolerance remains unresolved. Healthy individuals and subjects with liver cirrhosis were studied on two occasions: 1) an oral glucose tolerance test was performed, and 2) insulin secretion was inhibited and glucose was infused in a pattern and amount mimicking the systemic delivery rate of glucose after a carbohydrate meal. Insulin was concurrently infused to mimic a healthy postprandial insulin profile. Postabsorptive glucose concentrations were equal (5.36 +/- 0.12 vs. 5.40 +/- 0.25 mmol/l, P = 0.89), despite higher insulin (P < 0.01), C-peptide (P < 0.01), and free fatty acid (P = 0.05) concentrations in cirrhotic than in control subjects. Endogenous glucose release (EGR; 11.50 +/- 0.50 vs. 11.73 +/- 1.00 mumol.kg(-1). min(-1), P = 0.84) and the contribution of gluconeogenesis to EGR (6.60 +/- 0.47 vs. 6.28 +/- 0.64 mumol.kg(-1). min(-1), P = 0.70) were unaltered by cirrhosis. A minimal model recently developed for the oral glucose tolerance test demonstrated an impaired insulin sensitivity index (P < 0.05), whereas the beta-cell response to glucose was unaltered (P = 0.72). During prandial glucose and insulin infusions, the integrated glycemic response was greater in cirrhotic than in control subjects (P < 0.05). EGR decreased promptly and comparably in both groups, but glucose disappearance was insufficient at the prevailing glucose concentration (P < 0.05). Moreover, identical rates of [3-(3)H]glucose infusion produced higher tracer concentrations in cirrhotic than in control subjects (P < 0.05), implying a defect in glucose uptake. In conclusion, carbohydrate intolerance in liver cirrhosis is determined by insulin resistance and the ability of glucose to stimulate insulin secretion. During prandial glucose and insulin concentrations, EGR suppression was unaltered, but glucose uptake was impaired, which demonstrates that intolerance can be ascribed to a defect in glucose uptake, rather than abnormalities in glucose production or beta-cell function. Although insulin secretion ameliorates glucose intolerance, impaired glucose uptake during physiological glucose and insulin concentrations produces marked and sustained hyperglycemia, despite concurrent abnormalities in glucose production or insulin secretion.
A fast L-R comparison system by digital sampling measurement approach

A digital sampling system which can fast compare inductors with ac standard resistors in the frequency range between 20 Hz and 20 kHz is described. It can also precisely measure inductance at heavy current or high voltage. Inductors from 10mH to 10H in the low audio frequency range can be measured with the least relative uncertainty of 50 to 100 parts in 106.
Joint user pairing and power allocation for downlink non-orthogonal multiple access systems

Downlink non-orthogonal multiple access (NOMA), where users are paired as user set and multiplexed in the power domain, is a promising technology for fifth generation (5G) communication system. This paper studies joint optimization of user pairing and power allocation to maximize generalized proportional fair metric subject to transmit power constraints. This problem can be divided into two parts: user pairing and power allocation. In order to reduce the computation burden, we present a pre-defined multi-user pairing criterion to exclude user sets, which are unsuitable for multiplexing. Furthermore, for a given user set, a low complexity multi-user power allocation scheme is proposed by exploiting the convexity of the optimization problem. Simulation results show that the proposed user pairing and power allocation scheme can significantly enhance the downlink system performance and reduce complexity compared to the existing schemes in NOMA systems.
A Literature Survey of Topology Control and Its Related Issues in Wireless Sensor Networks

Issues of Topology control (TC) have captured more attentions in Wireless Sensor Networks (WSN). While WSN applications are normally optimized by the underlying network topology. Now a day's WSNs is one of the most interesting areas of research and are universally being used and deployed or implements to monitor the surrounding physical environments. A number of approaches have been invested in wireless sensor networking, such as topology directed routing, sensor coverage based TC and network connectivity based TC. Many schemes have proved to be able to provide a better network monitoring and communication performance with prolonged system lifetime. In this survey paper, it provides a view of the studies in the area of WSN with different topology issues. By summarizing previous achievements and analyzing existed problems, we provide some idea within this field and also point out some research direction for the future.
Oligophrenin-1, a Rho GTPase-activating protein (RhoGAP) involved in X-linked mental retardation, is expressed in the enteric nervous system.

Oligophrenin-1 is a RhoGTPase-activating protein (RhoGAP) that is involved in the regulation of shape changes in dendritic spines, and outgrowth of axons and dendrites in the brain. These changes in neuronal morphology are central to the mechanisms of plasticity, learning, and memory. Although the enteric nervous system also exhibits long-term changes in neuronal function, the expression and involvement of oligophrenin-1 has not previously been investigated. We show by RT-PCR analysis that oligophrenin-1 mRNA is expressed in the myenteric plexus (MP) of the guinea pig ileum. Sequencing of RT-PCR products showed that guinea pig oligophrenin-1 mRNA is 98% and 87% homologous to human and mouse oligophrenin-1, respectively, except that a 42 bp sequence is absent from the guinea pig mRNA. This 42 bp sequence codes for a sequence of 14 amino acids located near the carboxy-terminal end of the RhoGAP domain in the human sequence. An antibody that recognizes human oligophrenin-1 identified a 91 kDa protein band in rat and mouse brain lysates and in guinea pig sciatic nerve, and a 36 kDa protein band in both purified enteric ganglion cell and brain lysate from guinea pig. Oligophrenin-1 is localized specifically to neurons and varicose axons in the MPs and submucosal plexuses (SMPs) of the guinea pig and rat, but is not detectable in glial cells, smooth muscle, or other cell types. These findings indicate that oligophrenin-1 is expressed in the enteric nervous system, where it may regulate morphological changes in axons and dendrites, and thus modulate neuronal connectivity.
Predictors of Health-Related Quality of Life Among Patients With Myocardial Infarction

This cross-sectional correlational study aimed to examine health-related quality of life (HRQoL) and its predictors among patients with myocardial infarction (MI). One hundred and twenty-eight outpatients with MI were recruited from a university hospital. The 12-item Short-Form Health Survey version 2, Myocardial Infarction Dimensional Assessment Scale (MIDAS), and Hospital Anxiety and Depression Scale (HADS) were used to measure the study variables. Compared with the findings of similar studies of patients with MI, this sample, despite having significant coronary risk factors, reported generally better HRQoL. Predictors of physical HRQoL included low monthly household income, whereas predictors of mental HRQoL included ex-smoker, alcohol use, hypertension, anxiety, and depression. Special attention may need to be given to those people with a low income level, who are ex-smokers, use alcohol, or have hypertension, anxiety, or depression.
Swimming pools and fungi: An environmental epidemiology survey in Italian indoor swimming facilities

Abstract A growing number of people attend swimming facilities for recreational activities, rehabilitative treatments, or sport. Filamentous fungi and yeast can be isolated from contaminated air, water and surfaces and may represent a biological risk for employees and users. Here we investigated the occurrence of mycotic species, in a sample of Italian swimming pools (n = 10). Detection and identification of isolated species were achieved by cultural and morphological methods. Results revealed moderate mycotic titres and a high biodiversity. Penicillium spp. , Aspergillus spp. , Cladosporium spp. and Alternaria sp. , were constantly detected in air and surfaces sampled by the swimming area, while pathogenic yeast Candida albicans was never detected. Fusarium spp. was the most common taxon isolated from surfaces. For one facility, we typed the genotypic profiles and studied, by genetic typing, the spatial and temporal distribution of isolates. Phylogenetic relationships between species were analysed by alignment of small ribosomal subunit RNA sequences.
Peptide anchoring spore coat assembly to the outer forespore membrane in Bacillus subtilis

Spore formation in Bacillus subtilis involves the formation of a thick, proteinaceous shell or coat that is assembled around a specialized membrane known as the outer forespore membrane. Here we present evidence that the assembling coat is tethered to the outer forespore membrane by a 26‐amino‐acid peptide called SpoVM, which is believed to form an amphipathic helix. We show that proper localization of SpoVM is dependent on SpoIVA, a morphogenetic protein that forms the basement layer of the spore coat, and conversely, that proper localization of SpoIVA is dependent on SpoVM. Genetic, biochemical and cytological evidence indicates that this mutual dependence is mediated in part by contact between an amino acid side‐chain located near the extreme C‐terminus of SpoIVA and an amino acid side‐chain on the hydrophilic face of the SpoVM helix. Evidence is also presented that SpoVM adheres to the outer forespore membrane via hydrophobic, amino acid side‐chains on the hydrophobic face of the helix. The results suggest that the SpoVM helix is oriented parallel to the membrane with the hydrophobic face buried in the lipid bilayer.
Decreased Circulating Klotho Levels in Patients Undergoing Dialysis and Relationship to Oxidative Stress and Inflammation

♦ Introduction: It has been reported that klotho deficiency is associated with oxidative stress and inflammation in experimental kidney disease models. Patients with endstage renal disease (ESRD) are particularly characterized by increased oxidative stress and inflammation. However, little is known about the relationship between these features and klotho in patients with ESRD. ♦ Methods: We conducted a single-center, cross-sectional study of 78 patients receiving peritoneal dialysis (PD). Serum concentrations of klotho, high-sensitivity C-reactive protein (hsCRP), interleukin-6 (IL-6), and 8-isoprostane were measured by enzyme-linked immunosorbent assay. To define factors independently associated with klotho, we determined Spearman’s correlation coefficients for between co-variates and conducted multiple linear regression analyses. ♦ Results: Patients were classified by median concentration of klotho. In patients with klotho levels > 329.6 pg/mL, serum 8-isoprostane and IL-6 levels were significantly higher than in those with klotho levels < 329.6 pg/mL. In correlation analyses, log 8-isoprostane (γ = –0.310, p = 0.006) and log IL-6 (γ = –0.343, p = 0.002) were inversely correlated with log klotho. After adjustment for age, gender, mean arterial pressure, log intact parathyroid hormone, and log IL-6, log 8-isoprostane was independently associated with log klotho (β = –0.158, p = 0.040). However, the significant relationship between klotho and IL-6 was not seen in an adjusted model. ♦ Conclusions: This study showed that circulating klotho levels were significantly associated with 8-isoprostane levels in patients undergoing PD, suggesting a potential link between klotho deficiency and enhanced oxidative stress in ESRD patients.
Finiteness and rational sequences, constructively*

Abstract Rational sequences are possibly infinite sequences with a finite number of distinct suffixes. In this paper, we present different implementations of rational sequences in Martin–Löf type theory. First, we literally translate the above definition of rational sequence into the language of type theory, i.e., we construct predicates on possibly infinite sequences expressing the finiteness of the set of suffixes. In type theory, there exist several inequivalent notions of finiteness. We consider two of them, listability and Noetherianness, and show that in the implementation of rational sequences the two notions are interchangeable. Then we introduce the type of lists with backpointers, which is an inductive implementation of rational sequences. Lists with backpointers can be unwound into rational sequences, and rational sequences can be truncated into lists with backpointers. As an example, we see how to convert the fractional representation of a rational number into its decimal representation and vice versa.
HotelOpinion: An opinion mining system on hotel reviews in Thailand

This paper reports on the extension of our previous work on feature-based opinion mining for Thai language. In this paper, we present an approach for automatically constructing two main lexicons: features and polar words based on syntactic pattern analysis. The evaluation is performed with a case study on hotel reviews. The experimental results show that our approach is effective in performing its task. To illustrate the potential application, we implement a system called HotelOpinion for summarizing the hotel reviews written in the Thai language. Our system can also generate a comparison between hotels based upon the user's preferred features and then present the results in a user-friendly visualization. Results from our system can be used to determine public perceptions regarding selected hotels in order to allow the business to improve their customer intimacy and satisfaction.