Miracle-dz/UniFAR-FTUs huggingface dataset:
Prognostic Impacts of Hypoxic Markers in Soft Tissue Sarcoma

Background. We aimed to explore the prognostic impact of the hypoxia-induced factors (HIFαs) 1 and 2, the metabolic HIF-regulated glucose transporter GLUT-1, and carbonic anhydrase IX (CAIX) in non-gastrointestinal stromal tumor soft tissue sarcomas (non-GIST STS). Methods. Duplicate cores with viable tumor tissue from 206 patients with non-GIST STS were obtained and tissue microarrays were constructed. Immunohistochemistry (IHC) was used to evaluate expression of hypoxic markers. Results. In univariate analyses, GLUT-1 (P < 0.001) and HIF-2α (P = 0.032) expression correlated significantly with a poor disease-specific survival (DSS). In the multivariate analysis, however, only high expression of GLUT-1 (HR 1.7, CI 95% 1.1–2.7, P = 0.021) was a significant independent prognostic indicator of poor DSS. Conclusion. GLUT-1 is a significant independent negative prognostic factor in non-GIST STS.
Load balancing and pricing for spectrum access control in cognitive radio networks

In dynamic spectrum access (DSA) control, the prevalent approach to provide economics incentives for operators is pricing, whereas load balancing gives congestion-avoidance incentives to secondary users (SUs). Despite complexities of i) the couplings between pricing, load balancing and SUs' spectrum access decision, and ii) the heterogeneity of primary users' traffic and SUs types, we propose to solve the joint load balancing and pricing problem to maximize operator' revenue in a monopoly market. In this market, we first show there exists a unique SUs' equilibrium arrival rate to the monopolist's channels, and then we show that the joint problem can be solved efficiently by exploiting its convex structure. We next propose a low-complexity algorithm that enable the operator to maximize its revenue.
Two new sea surface temperature anomalies indices for capturing the eastern and central equatorial Pacific type El Niño‐Southern Oscillation events during boreal summer

Using monthly mean data from the Hadley Center and the National Centers for Environmental Prediction‐National Center for Atmospheric Research (NCEP‐NCAR) reanalysis, we have constructed two new indices ICP and IEP of boreal summer sea surface temperature anomalies (SSTA) in equatorial Pacific for period of 1963–2016 by employing methods including the six‐order polynomial fitting and pattern correlations. The new indices ICP and IEP are almost independent of each other. Using these two indices, we are able to successfully capture the main features of central Pacific (CP) and eastern Pacific (EP) type SSTA variations in tropical Pacific in both spatial and temporal. The EP‐type SSTA events vary on inter‐annual timescales whereas CP‐type events vary on both inter‐annual and inter‐decadal. For the CP‐type events, stronger positive (negative) SST anomalies are observed in central tropical Pacific while weaker SSTA in the Maritime Continent (MC) and eastern equatorial Pacific during positive (negative) phase of index ICP. However, For EP‐type events, the stronger SSTAs appear in both the equatorial Pacific region east of dateline and Peruvian coastal ocean while weaker SSTAs in MC and western equatorial Pacific regions. Both the anomalous heating induced by CP‐ and EP‐type SSTA may force the atmosphere to respond, resulting in different types of anomalous patterns of circulations, rainfall, and near‐surface air temperatures. These results indicate that the new indexes are useful for our better investigating the CP‐ and EP‐type summer SSTA events as well as their climate impacts, thereby providing a clue to monitoring and predicting strong SSTA events in equatorial Pacific.
Mechanism by which a recently discovered allosteric inhibitor blocks glutamine metabolism in transformed cells

Significance The work described here was motivated by our previous discovery of a connection between Rho GTPase activation and the up-regulation of mitochondrial glutaminase C (GAC), which is responsible for satisfying the glutamine addiction of cancer cells. This connection was originally established by our identification of a lead compound, 968, for a new class of inhibitors of oncogenic transformation. Although GAC was identified as the putative target for 968, how it regulated GAC was poorly understood. Here we provide important insights into the actions of 968, through the development of novel assays for its direct binding to GAC and its effects on enzyme activity. These findings offer exciting new strategies for interfering with the metabolic reprogramming critical for malignant transformation. The mitochondrial enzyme glutaminase C (GAC) catalyzes the hydrolysis of glutamine to glutamate plus ammonia, a key step in the metabolism of glutamine by cancer cells. Recently, we discovered a class of allosteric inhibitors of GAC that inhibit cancer cell growth without affecting their normal cellular counterparts, with the lead compound being the bromo-benzophenanthridinone 968. Here, we take advantage of mouse embryonic fibroblasts transformed by oncogenic Dbl, which hyperactivates Rho GTPases, together with 13C-labeled glutamine and stable-isotope tracing methods, to establish that 968 selectively blocks the enhancement in glutaminolysis necessary for satisfying the glutamine addiction of cancer cells. We then determine how 968 inhibits the catalytic activity of GAC. First, we developed a FRET assay to examine the effects of 968 on the ability of GAC to undergo the dimer-to-tetramer transition necessary for enzyme activation. We next demonstrate how the fluorescence of a reporter group attached to GAC provides a direct read-out of the binding of 968 and related compounds to the enzyme. By combining these fluorescence assays with newly developed GAC mutants trapped in either the monomeric or dimeric state, we show that 968 has the highest affinity for monomeric GAC and that the dose-dependent binding of 968 to GAC monomers directly matches its dose-dependent inhibition of enzyme activity and cellular transformation. Together, these findings highlight the requirement of tetramer formation as the mechanism of GAC activation and shed new light on how a distinct class of allosteric GAC inhibitors impacts the metabolic program of transformed cells.
Identification of a Novel, Dendritic Cell-associated Molecule, Dectin-1, by Subtractive cDNA Cloning*

Dendritic cells (DC) are special subsets of antigen presenting cells characterized by their potent capacity to activate immunologically naive T cells. By subtracting the mRNAs expressed by the mouse epidermus-derived DC line XS52 with the mRNAs expressed by the J774 macrophage line, we identified five novel genes that were expressed selectively by this DC line. One of these genes encoded a type II membrane-integrated polypeptide of 244 amino acids containing a putative carbohydrate recognition domain motif at the COOH-terminal end. This molecule, termed “dectin-1,” was expressed abundantly at both mRNA and protein levels by the XS52 DC line, but not by non-DC lines (including the J774 macrophage line). Dectin-1 mRNA was detected predominantly in spleen and thymus (by Northern blotting) and in skin-resident DC, i.e. Langerhans cells (by reverse transcription-polymerase chain reaction). Affinity-purified antibody against dectin-1 identified a 43-kDa glycoprotein in membrane fractions isolated from the XS52 DC line and from the dectin-1 cDNA-transfected COS-1 cells. His-tagged recombinant proteins containing the extracellular domains of dectin-1 showed marked and specific binding to the surface of T cells and promoted their proliferation in the presence of anti-CD3 monoclonal antibody at suboptimal concentrations. These in vitro results suggest that dectin-1 on DC may bind to as yet undefined ligand(s) on T cells, thereby delivering T cell co-stimulatory signals. Not only do these results document the efficacy of subtractive cDNA cloning for the identification of unique genes expressed by DC, they also provide a framework for studying the physiological function of dectin-1.
Opposing Roles of Membrane and Soluble Forms of the Receptor for Advanced Glycation End Products in Primary Respiratory Syncytial Virus Infection

Respiratory syncytial virus (RSV), a common respiratory pathogen in infants and the older population, causes pulmonary inflammation and airway occlusion that leads to impairment of lung function. Here, we have established a role for receptor for advanced glycation end products (RAGE) in RSV infection. RAGE-deficient (ager−/−) mice were protected from RSV-induced weight loss and inflammation. This protection correlated with an early increase in type I interferons, later decreases in proinflammatory cytokines, and a reduction in viral load. To assess the contribution of soluble RAGE (sRAGE) to RSV-induced disease, wild-type and ager−/− mice were given doses of sRAGE following RSV infection. Of interest, sRAGE treatment prevented RSV-induced weight loss and neutrophilic inflammation to a degree similar to that observed in ager−/− mice. Our work further elucidates the roles of RAGE in the pathogenesis of respiratory infections and highlights the opposing roles of membrane and sRAGE in modulating the host response to RSV infection.
Hermitian Polynomial for Speaker Adaptation of Connectionist Speech Recognition Systems

Model adaptation techniques are an efficient way to reduce the mismatch that typically occurs between the training and test condition of any automatic speech recognition (ASR) system. This work addresses the problem of increased degradation in performance when moving from speaker-dependent (SD) to speaker-independent (SI) conditions for connectionist (or hybrid) hidden Markov model/artificial neural network (HMM/ANN) systems in the context of large vocabulary continuous speech recognition (LVCSR). Adapting hybrid HMM/ANN systems on a small amount of adaptation data has been proven to be a difficult task, and has been a limiting factor in the widespread deployment of hybrid techniques in operational ASR systems. Addressing the crucial issue of speaker adaptation (SA) for hybrid HMM/ANN system can thereby have a great impact on the connectionist paradigm, which will play a major role in the design of next-generation LVCSR considering the great success reported by deep neural networks - ANNs with many hidden layers that adopts the pre-training technique - on many speech tasks. Current adaptation techniques for ANNs based on injecting an adaptable linear transformation network connected to either the input, or the output layer are not effective especially with a small amount of adaptation data, e.g., a single adaptation utterance. In this paper, a novel solution is proposed to overcome those limits and make it robust to scarce adaptation resources. The key idea is to adapt the hidden activation functions rather than the network weights. The adoption of Hermitian activation functions makes this possible. Experimental results on an LVCSR task demonstrate the effectiveness of the proposed approach.
A visibility determination algorithm for interactive virtual endoscopy

We present a new visibility determination algorithm for interactive virtual endoscopy. The algorithm uses a modified version of template-based ray casting to extract a view dependent set of potentially visible voxels from volume data. The voxels are triangulated by Marching Cubes and the triangles are rendered onto the display by a graphics accelerator. Early ray termination and space leaping are used to accelerate the ray casting step and a quadtree subdivision algorithm is used to reduce the number of cast rays. Compared to other recently proposed rendering algorithms for virtual endoscopy, our rendering algorithm does not require a long preprocessing step or a high-end graphics workstation, but achieves interactive frame rates on a standard PC equipped with a low-cost graphics accelerator.
Highly efficient transfection system for functional gene analysis in adult amphibian lens regeneration

The analysis of newt lens regeneration has been an important subject in developmental biology. Recently, it has been reported that the genes involved in the normal eye development are also expressed in the regenerative process of lens regeneration in the adult newt. However, functional analysis of these genes has not been possible, because there is no system to introduce genes efficiently into the cells involved in the regeneration. In the present study, lipofection was used as the method for gene transfer in cultured pigmented iris cells that can transdifferentiate into lens cells in newt lens regeneration. Positive expression of a reporter gene was obtained in more than 70% of cells. In addition, the aggregate derived from gene‐transfected cells maintained its expression at a high level for a long time within the host tissue. To verify the effectiveness of this model system with a reporter gene in lens regeneration, Pax6, which is suggested to be involved in normal eye development and lens regeneration, was transfected. Ectopic expression of lens‐specific crystallins was obtained in cells that show no such activity in normal lens regeneration. These results made it possible for the first time to analyze the molecular mechanism of lens regeneration in the adult newt.
Respiratory Sinus Arrhythmia Reactivity in Current and Remitted Major Depressive Disorder

Objective Low resting respiratory sinus arrhythmia (RSA) levels and blunted RSA reactivity are thought to index impaired emotion regulation capacity. Major depressive disorder (MDD) has been associated with aberrant RSA reactivity and recovery to a speech stressor task relative to healthy controls. Whether impaired RSA functioning reflects aspects of the depressed mood state or a stable vulnerability marker for depression is unknown. Methods We compared resting RSA and RSA reactivity between adults with MDD (n = 49), remitted depression (RMD, n = 24), and healthy controls (n = 45). Electrocardiogram data were collected during a resting baseline, a paced-breathing baseline, and two reactivity tasks (speech stressor, cold exposure). Results A group by time quadratic effect emerged (F(2,109) = 4.36, p = . 015) for RSA across phases of the speech stressor (baseline, instruction, preparation, speech, recovery). Follow-up analyses revealed that those with MDD uniquely exhibited blunted RSA reactivity, whereas RMD and controls both exhibited the anticipated task-related vagal withdrawal and posttask recovery. The group by time interaction remained after covariation for age, sex, waist circumference, physical activity, and respiration, but not sleep quality. Conclusions These results provide new evidence that aberrant RSA reactivity marks features that track the depressed state, such as poor sleep, rather than a stable trait evident among asymptomatic persons.
Effect of rice straw and/or nitrogen fertiliser inputs on methanogenic archaeal and denitrifying communities in a typical rice paddy soil

ABSTRACT To understand better the microbial functional populations which are involved in methanogenesis and denitrification in paddy soils with rice straw (RS) and/or nitrogen fertiliser (potassium nitrate, N) application, the dynamics of methanogens and the denitrifying community were monitored simultaneously during the incubation period. The results show that the community structure of methanogens remained relatively stable among treatments based on 16S rDNA analysis, but fluctuated based on 16S rRNA. The Methanocellaceae and Methanosarcinaceae dominated all treatments at 16S rDNA and 16S rRNA level, respectively. RS+N increased the relative abundance of Methanosaetaceae at the 16S rRNA level, while there was an increasing trend in that Methanomicrobiaceae following RS addition at the 16S rDNA level. RS and/or N did not significantly change the diversity of methanogens targeting both 16S rDNA and 16S rRNA. RS and RS+N increased copy numbers of methanogens targeting both 16S rDNA and 16S rRNA analyses. The community structure and abundance of nirS and nosZ-containing denitrifiers, and the diversity of nirS-containing denitrifiers was significantly altered only by the N treatment. These results indicate that the community structure, diversity and abundance of methanogens respond differently to RS addition at the 16S rDNA and 16S rRNA levels.
Lyapunov-Razumikhin and Lyapunov-Krasovskii theorems for interconnected ISS time-delay systems

We consider an arbitrary number of intercon- nected nonlinear systems with time-delays and investigate them in view of input-to-state stability (ISS). The useful tools for single time-delay systems, the ISS Lyapunov-Razumikhin func- tions and ISS Lyapunov-Krasovskii functionals are redefined and applied to interconnected systems. By the help of a small- gain condition we prove that the whole system with time-delays has the ISS property, if each subsystem has an ISS Lyapunov- Razumikhin function or ISS Lyapunov-Krasovskii functional. Furthermore we construct the ISS Lyapunov-Razumikhin (- Krasovskii) function(al) and the corresponding gains of the whole system. I. INTRODUCTION
Effects of exercise before or after meal ingestion on fat balance and postprandial metabolism in overweight men

It is unclear how timing of exercise relative to meal ingestion influences substrate balance and metabolic responses. The present study aimed to compare the effects of exercise performed before or after breakfast on fat balance and postprandial metabolism. A total of ten sedentary overweight men (aged 28·1 (sem 10·7) years, BMI 29·0 (sem 2·8) kg/m2) underwent three trials in random order involving: (1) performing no exercise (CON), or walking for 60 min at 50 % maximal O2 uptake either (2) before (Ex-Meal) or (3) after (Meal-Ex) consuming a standardised breakfast meal. In each trial an ad libitum lunch was provided 3·5 h after breakfast. Substrate utilisation was assessed by indirect calorimetry and blood was taken at regular intervals over an 8·5 h observation period. At the end of the observation period, fat balances in the Ex-Meal ( − 1043 (sem 270) kJ) and Meal-Ex ( − 697 (sem 201) kJ) trials were both significantly lower than CON (204 (sem 165) kJ) and fat balance in the Ex-Meal trial was significantly lower than in the Meal-Ex trial (all P <0·0001). Compared with the CON trial, the 8·5 h postprandial TAG response was only significantly lowered in the Ex-Meal trial ( − 17 %, P =0·025) and not in the Meal-Ex trial ( − 11 %, P =0·20). Both the Ex-Meal and Meal-Ex trials showed significantly lowered insulin responses relative to the CON trial (by 19 and 24 %, respectively, P <0·01 for both). There were no differences in lunch energy intake between trials. The present findings suggest that there may be an advantage for body fat regulation and lipid metabolism in exercising before compared with after breakfast. However, further study is needed to determine whether the present findings extend over the long term under free-living conditions.
Occurrence and behaviour of persistent lipophilic contaminants in the Southern Hemisphere.

Lipophilic substances, having environmental persistence and occurring widely in ecosystems, have been generally described as persistent lipophilic contaminants (PLCs) or persistent organic pollutants (POPs). These include the semivolatile and persistent chlorohydrocarbon pesticides, such as DDT, HCH’s, dieldrin and chlordane, and industrial chlorohydrocarbons such as the PCBs and HCB, which were detected throughout environmental compartments and were found to be bioaccumulative in lipid-containing tissues (Woodwell et al, 1971). In addition, there have been combustion product residues detected consisting principally of the polychlorodibenzodioxins (PCDDs ) and the polychlorodibenzofurans (PCDFs) which share the persistent, lipophilic and bioaccumulative properties of the chlorohydrocarbons (Rappe et al, 1978). Thus, currently the following substances are usually considered to be globally important PLCs: chlordane, DDT, dieldrin, endrin, heptachlor, hexachlorobenzene (HCB), hexachlorocyclohexane (HCH including lindane), mirex, polychlorobiphenyls (PCBs), PCDDs, PCDFs and toxaphene. In recent years, residues of such substances as the polycyclic aromatic hydrocarbons (PAHs), endosulfan, atrazine and many other substances have been detected in many sectors of the environment and share many of the attributes of PLCs (for example Yang et al, 1991) Investigations and studies in the 1980s and 90s have identified long-range transport through the atmosphere, primarily in the Northern Hemisphere, as a mechanism which is important in the distribution of these substances. Recent studies have focused on the global distribution of PLCs and hypotheses such as the “grasshopper effect” have been proposed to explain the nature of the distribution of some PLCs from lower to higher latitudes (eg. equatorial to polar regions) particularly in the Northern Hemisphere (Mackay and Wania, 1995). The significance of the usage patterns and distributions of PLCs and other related compounds within countries and geographical regions of the Southern Hemisphere remains much less clear. The objectives of this investigation were to evaluate the data available on PLCs and other compounds producing residues in the Southern Hemisphere and to evaluate temporal changes and assess the processes of global distribution.
Techniques for Classifying Executions of Deployed Software to Support Software Engineering Tasks

There is an increasing interest in techniques that support analysis and measurement of fielded software systems. These techniques typically deploy numerous instrumented instances of a software system, collect execution data when the instances run in the field, and analyze the remotely collected data to better understand the system's in-the-field behavior. One common need for these techniques is the ability to distinguish execution outcomes (e.g., to collect only data corresponding to some behavior or to determine how often and under which condition a specific behavior occurs). Most current approaches, however, do not perform any kind of classification of remote executions and either focus on easily observable behaviors (e.g., crashes) or assume that outcomes' classifications are externally provided (e.g., by the users). To address the limitations of existing approaches, we have developed three techniques for automatically classifying execution data as belonging to one of several classes. In this paper, we introduce our techniques and apply them to the binary classification of passing and failing behaviors. Our three techniques impose different overheads on program instances and, thus, each is appropriate for different application scenarios. We performed several empirical studies to evaluate and refine our techniques and to investigate the trade-offs among them. Our results show that 1) the first technique can build very accurate models, but requires a complete set of execution data; 2) the second technique produces slightly less accurate models, but needs only a small fraction of the total execution data; and 3) the third technique allows for even further cost reductions by building the models incrementally, but requires some sequential ordering of the software instances' instrumentation.