Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Infection with Salmonella enterica

ABSTRACT To investigate the extent to which macrophages respond to Salmonella infection, we infected RAW 264.7 macrophages with Salmonella enterica serotype Typhimurium and analyzed macrophage proteins at various time points following infection by using a global proteomic approach. A total of 1,006 macrophage and 115 Salmonella proteins were identified with high confidence. Most of the Salmonella proteins were observed in the late stage of the infection time course, which is consistent with the fact that the bacterial cells proliferate inside RAW 264.7 macrophages. The peptide abundances of most of the identified macrophage proteins remained relatively constant over the time course of infection. Compared to those of the control, the peptide abundances of 244 macrophage proteins (i.e., 24% of the total identified macrophage proteins) changed significantly after infection. The functions of these Salmonella-affected macrophage proteins were diverse, including production of antibacterial nitric oxide (i.e., inducible nitric oxide synthase), production of prostaglandin H2 (i.e., cyclooxygenase 2), and regulation of intracellular traffic (e.g., sorting nexin 5 [SNX5], SNX6, and SNX9). Diverse functions of the Salmonella-affected macrophage proteins demonstrate a global macrophage response to Salmonella infection. Western blot analysis not only confirmed the proteomic results for a selected set of proteins but also revealed that (i) the protein abundance of mitochondrial superoxide dismutase increased following macrophage infection, indicating an infection-induced oxidative stress in mitochondria, and (ii) in contrast to infection of macrophages by wild-type Salmonella, infection by the sopB deletion mutant had no negative impact on the abundance of SNX6, suggesting a role for SopB in regulating the abundance of SNX6.
Risk of nonmelanoma skin cancer with azathioprine use

While often life‐saving for many complex diseases, iatrogenic immunosuppression has been associated with life‐threatening infections and malignancies. Among these malignancies is skin cancer. Skin cancer is the most common form of cancer in the United States; the nonmelanoma skin cancers have an annual incidence of greater than 1,000,000 people in the US. It is well documented that the risk of nonmelanoma skin cancer (NMSC) is increased in those who are immunosuppressed. While many articles have been published on skin cancer risk in organ transplant recipients, little has been written regarding the incidence of nonmelanoma skin cancer in inflammatory bowel disease. A review of the literature of patients who are immunosuppressed for autoimmune disorders, and specifically, inflammatory bowel diseases, is discussed, as well as clinical presentations and treatment options.
Repeated high‐intensity exercise modulates Ca2+ sensitivity of human skeletal muscle fibers

The effects of short‐term high‐intensity exercise on single fiber contractile function in humans are unknown. Therefore, the purposes of this study were: (a) to access the acute effects of repeated high‐intensity exercise on human single muscle fiber contractile function; and (b) to examine whether contractile function was affected by alterations in the redox balance. Eleven elite cross‐country skiers performed four maximal bouts of 1300 m treadmill skiing with 45 min recovery. Contractile function of chemically skinned single fibers from triceps brachii was examined before the first and following the fourth sprint with respect to Ca2+ sensitivity and maximal Ca2+‐activated force. To investigate the oxidative effects of exercise on single fiber contractile function, a subset of fibers was incubated with dithiothreitol (DTT) before analysis. Ca2+ sensitivity was enhanced by exercise in both MHC I (17%, P < 0.05) and MHC II (15%, P < 0.05) fibers. This potentiation was not present after incubation of fibers with DTT. Specific force of both MHC I and MHC II fibers was unaffected by exercise. In conclusion, repeated high‐intensity exercise increased Ca2+ sensitivity in both MHC I and MHC II fibers. This effect was not observed in a reducing environment indicative of an exercise‐induced oxidation of the human contractile apparatus.
How well can the accuracy of comparative protein structure models be predicted?

Comparative structure models are available for two orders of magnitude more protein sequences than are experimentally determined structures. These models, however, suffer from two limitations that experimentally determined structures do not: They frequently contain significant errors, and their accuracy cannot be readily assessed. We have addressed the latter limitation by developing a protocol optimized specifically for predicting the Cα root‐mean‐squared deviation (RMSD) and native overlap (NO3.5Å) errors of a model in the absence of its native structure. In contrast to most traditional assessment scores that merely predict one model is more accurate than others, this approach quantifies the error in an absolute sense, thus helping to determine whether or not the model is suitable for intended applications. The assessment relies on a model‐specific scoring function constructed by a support vector machine. This regression optimizes the weights of up to nine features, including various sequence similarity measures and statistical potentials, extracted from a tailored training set of models unique to the model being assessed: If possible, we use similarly sized models with the same fold; otherwise, we use similarly sized models with the same secondary structure composition. This protocol predicts the RMSD and NO3. 5Å errors for a diverse set of 580,317 comparative models of 6174 sequences with correlation coefficients (r) of 0.84 and 0.86, respectively, to the actual errors. This scoring function achieves the best correlation compared to 13 other tested assessment criteria that achieved correlations ranging from 0.35 to 0.71.
Power-quality model based on IGBT dynamic-conduction for non-polluting lighting applications

In this paper, a power-quality model based on dynamic-conduction of the modern switching power devices is presented. The power-quality analysis is needed due to the serious problems by the compact fluorescent lamps (CFL) technology, including generation of poor power-quality and the risks on the human health because the CFL contain mercury. The proposed model utilizes normalized symbolic functions of the current conduction functions defined by closed time intervals, which has been applied to a single-phase AC-DC converter. Also, the total harmonic distortion (THD) is evaluated to demonstrate the improvement of the power quality as a function of the normalized Fourier coefficients. The principle of operation of the single-phase AC-DC converter is presented and the results indicate that power quality would be enhanced using incandescent lamps with lower power consumption.
Policy graph pruning and optimization in Monte Carlo Value Iteration for continuous-state POMDPs

Nowadays, Partially Observation Markov Decision Processes (POMDPs) provide a principled mathematical framework for solving some realistic problems with continuous spaces. The recently introduced Monte Carlo Value Iteration (MCVI) can tackle such problems with continuous state spaces. It uses a policy graph implicitly to represent the value function, instead of using a set of α-functions explicitly. However, the size of its graph would grow over time and it doesn't take any measure to optimize the graph. This makes it not applicable for the devices with limited resources such as wearable watches. This paper introduces three novel techniques to prune and optimize the policy graph obtained by MCVI. First, we optimize the internal structure of a policy graph G whenever a new node is added into the policy graph. Second, we evaluate the value of each node in G and prune the nodes dominated by others. Third, we prune the redundant nodes, meaning that they are not reachable from the initial action node in any optimal policy graph. Empirical results show that, on the corridor and musical chairs problems, our pruning and optimization methods are useful for constructing more compact policy graphs with comparable qualities.
Tight bounds for LDPC codes under MAP decoding

We present a new approach to the analysis of codes on graphs under symbol-maximum a posteriori probability (MAP) decoding. The approach is based on Guerra's interpolation technique for spin glasses. The basic idea is to consider a smooth interpolation between the original decoding problem, and a much simpler system in which each bit is retransmitted without coding through a (different) "effective" channel. Quite interestingly, the resulting expressions are strictly related to the density-evolution analysis of belief propagation decoding. The fundamental quantities involved in the interpolation procedure are, for instance, the same as in density evolution, i.e. densities of messages. Motivated by heuristic statistical mechanics results, we conjecture our bounds to be tight.
The Sound of Consciousness: Neural Underpinnings of Auditory Perception

The neural correlates of consciousness (NCC), i.e., patterns of brain activity that specifically accompany a particular conscious experience, have been investigated mainly in the visual system using particularly suited paradigms, such as binocular rivalry and multistable percepts in combination with neural recordings or neuroimaging. Through the same principles, we look here for possible NCC in the auditory modality exploiting the properties of the Deutsch's illusion, a stimulation condition in which a sequence of two specular dichotic stimuli presented in alternation causes an illusory segregation of pitch and side (ear of origin), which can yield up to four different auditory percepts per dichotic stimulus. Using magnetoencephalography in humans, we observed cortical activity specifically accompanying conscious experience of pitch inside an early bilateral network, including the Heschl's gyrus, the middle temporal gyrus, the right inferior, and the superior frontal gyri. The conscious experience of perceived side was instead accompanied by later activity observed bilaterally in the inferior parietal lobe and in the superior frontal gyrus. These results suggest that the NCC are not independent of stimulus features and modality and that, even at the higher cortical levels, the different aspects of a single perceptual scene may not be simultaneously processed.
Variation in Large‐Conductance, Calcium‐Activated Potassium Channels from Hair Cells Along the Chicken Basilar Papilla

The mechanism for electrical tuning in non‐mammalian hair cells rests within the widely diverse kinetics of functionally distinct, large‐conductance potassium channels (BK), thought to result from alternative splicing of the pore‐forming α subunit and variable co‐expression with an accessory β subunit. Inside‐out patches from hair cells along the chicken basilar papilla revealed ‘tonotopic’ gradations in calcium sensitivity and deactivation kinetics. The resonant frequency for the hair cell from which the patch was taken was estimated from deactivation rates, and this frequency reasonably matched that predicted from the originating cell's tonotopic location. The rates of deactivation for native BK channels were much faster than rates reported for cloned chicken BK channels including both α and β subunits. This result was surprising since patches were pulled from hair cells in the apical half of the papilla where β subunits are most highly expressed. Heterogeneity in the properties of native chicken BK channels implies a high degree of molecular variation and hinders our ability to identify those molecular constituents.
Efficacy Study of Broken Rice Maltodextrin in In Vitro Wound Healing Assay

Maltodextrins that contain both simple sugars and polymers of saccharides have been widely used as ingredients in food products and pharmaceutical delivery systems. To date, no much work has been reported on the applications of maltodextrin from broken rice (RB) sources. Therefore, the objective of this work was to investigate the in vitro wound healing efficacy of RB maltodextrin at different conditions. Wounds treated with lower dextrose equivalent (DE) range (DE 10–14) of maltodextrins at a concentration of 10% obtained from RB were found to be able to heal the wounds significantly faster (p < 0.01) than maltodextrin with higher DE ranges (DE 15–19 and DE 20–24) and concentrations of 5% and 20%. The findings from both BrdU and MTT assay further confirmed its wound healing properties as the NIH 3T3 fibroblast wounded cells were able to proliferate without causing cytotoxic effect when wounded cell was treated with maltodextrin. All these findings indicated that the RB maltodextrin could perform better than the commercial maltodextrin at the same DE range. This study showed that RB maltodextrins had better functionality properties than other maltodextrin sources and played a beneficial role in wound healing application.
Homoeopathy for delayed onset muscle soreness: a randomised double blind placebo controlled trial.

OBJECTIVE: To pilot a model for determining whether a homoeopathic medicine is superior to placebo for delayed onset muscle soreness (DOMS). DESIGN: Randomised double blind placebo controlled trial. SETTING: Physiotherapy department of a homoeopathic hospital. SUBJECTS: Sixty eight healthy volunteers (average age 30; 41% men) undertook a 10 minute period of bench stepping carrying a small weight and were randomised to a homoeopathic medicine or placebo. OUTCOME MEASURES: Mean muscle soreness in the five day period after the exercise test, symptom free days, maximum soreness score, days to no soreness, days on medication. RESULTS: The difference between group means was 0.17 in favour of placebo with 95% confidence intervals +/- 0.50. Similar results were found for other outcome measures. CONCLUSION: The study did not find benefit of the homoeopathic remedy in DOMS. Bench stepping may not be an appropriate model to evaluate the effects of a treatment on DOMS because of wide variation between subject soreness scores.
Randomized assessment of rapid endovascular treatment of ischemic stroke.

BACKGROUND Among patients with a proximal vessel occlusion in the anterior circulation, 60 to 80% of patients die within 90 days after stroke onset or do not regain functional independence despite alteplase treatment. We evaluated rapid endovascular treatment in addition to standard care in patients with acute ischemic stroke with a small infarct core, a proximal intracranial arterial occlusion, and moderate-to-good collateral circulation. METHODS We randomly assigned participants to receive standard care (control group) or standard care plus endovascular treatment with the use of available thrombectomy devices (intervention group). Patients with a proximal intracranial occlusion in the anterior circulation were included up to 12 hours after symptom onset. Patients with a large infarct core or poor collateral circulation on computed tomography (CT) and CT angiography were excluded. Workflow times were measured against predetermined targets. The primary outcome was the score on the modified Rankin scale (range, 0 [no symptoms] to 6 [death]) at 90 days. A proportional odds model was used to calculate the common odds ratio as a measure of the likelihood that the intervention would lead to lower scores on the modified Rankin scale than would control care (shift analysis). RESULTS The trial was stopped early because of efficacy. At 22 centers worldwide, 316 participants were enrolled, of whom 238 received intravenous alteplase (120 in the intervention group and 118 in the control group). In the intervention group, the median time from study CT of the head to first reperfusion was 84 minutes. The rate of functional independence (90-day modified Rankin score of 0 to 2) was increased with the intervention (53.0%, vs. 29.3% in the control group; P<0.001). The primary outcome favored the intervention (common odds ratio, 2.6; 95% confidence interval, 1.7 to 3.8; P<0.001), and the intervention was associated with reduced mortality (10.4%, vs. 19.0% in the control group; P=0.04). Symptomatic intracerebral hemorrhage occurred in 3.6% of participants in intervention group and 2.7% of participants in control group (P=0.75). CONCLUSIONS Among patients with acute ischemic stroke with a proximal vessel occlusion, a small infarct core, and moderate-to-good collateral circulation, rapid endovascular treatment improved functional outcomes and reduced mortality. (Funded by Covidien and others; ESCAPE ClinicalTrials.gov number, NCT01778335.).
Developmental Regulation in Adulthood: Age-Normative and Sociostructural Constraints as Adaptive Challenges

Acknowledgments List of tables and figures Introduction 1. Selectivity and failure compensation as fundamental requirements of human behavior and development 2. The life course as a context of action 3. Primary and secondary control across the life span 4. A model of developmental regulation across the life span 5. Developmental goals as organizers of developmental regulation 6. Developmental regulation in different life-course ecologies 7. Social comparisons as prototypical strategies in developmental regulation 8. Conclusions and prospects for future research References Indexes.
Sharing of Computations

The main purpose of the thesis is to develop a model enabling one to reason about various techniques for program optimization, in particular wrt. \ speedup and correctness. Moreover, several methods to increase the amount of sharing are discussed, and a new one (to be termed ''ultimate sharing'') is treated in detail. Concerning speedup, a main point is to factor out the reasons why a program transformation may yield more than a constant speedup. Concerning correctness, the interesting part is preservation of termination properties. This issue is mainly addressed for a logic language, where previous results from the literature are generalized -- but also for a functional language some (more limited) results are presented.
Analysis of cognitive radio spectrum access with finite user population

A new loss model for cognitive radio spectrum access with finite user population are presented, and exact solution for the model and its approximation for computation scalability are given. Our model provides the investigation of the delay performance of a cognitive radio system. We study the delay performance of a cognitive radio system under various primary traffic loads and spectrum band allocations.
A novel dynamic network architecture model based on stochastic geometry and game theory

In this paper, a novel paradigm of user-provided connectivity in wireless networks is introduced using certain class of wireless terminals that can be turned temporarily into access points at any time while connected to the Internet. We show that a DNA (Dynamic Network Architecture) model improves the connectivity and capacity of ultra-dense wireless access networks without need to reconfigure the network infrastructure. The DNA operators motivate terminals to participate in this concept by providing incentives. An example is to allow terminals to transmit additional free traffic volume if they share their free bandwidth by acting as access points. The DNA operators manage the dynamic network in order to maximize their own profit by adjusting jointly their price and incentive rate. In addition, we model the joint problem of operator pricing and user resource sharing as a non-cooperative game and the resulting game admits a unique Nash equilibrium solution. Simulation results show high gains in such networks for terminals acting as access points and operators.
A Novel Inpainting Algorithm based on Sparse Representation

Recent studies in sparse representations show a variety of applications in the field of image processing. Such as in image denoising, inpainting, compression and more. But always the size of the dictionary has a trade off between the approximation speed and accuracy. In this paper, a moving k-means based dictionary pruning algorithm is applied to the patches of the dictionary to discover an optimum number of dictionary elements for a given data set. This optimized dictionary size feature, will improve the convergence speed of the decomposition algorithm without compromising its approximation accuracy. It also increases the performance of the decomposition algorithm. Simulation results show that the proposed optimized dictionary selection with KSVD (K-means singular value decomposition) yield better image inpainting than traditional KSVD.
Certification and Authentication of Data Structures

We studyquery authentication schemes , algorithmic and cryptographic constructions that provid e efficient and secure protocols for verifying the results of q ueries over structured data in untrusted or adversarial data distribution environments. We formally d efine the problem in a new data query and authentication setting that involves general query types ans wered in the RAM model of computation, and put forward a new approach for designing secure query authen tication schemes that, through the new concept ofquery certification, aims to authenticate the validity of the answer , rather than the entire process that generates the answer. Our main results state that t his new authentication framework achieves generality, namely any query type admits a secure query authentication scheme, and also supports an important type ofmodularity, namely the authentication of general queries based on the e valuation of relations over the data elements is reduced to the authentic ation of set-membership queries. Thus, in addition to general possibility results under general assump tions and characterization results using existing cryptographic techniques, we contribute a clear separatio n between algorithmics and cryptography in data-authentication protocol design, and sufficient condi tions for achieving super-efficient answer verification in time asymptotically less than the time needed to a nswer the query.
TagScore: Approximate Similarity Using Tag Synopses

Collaborative tagging is the aggregate effort by a community of online users to annotate web content with metadata labels called tags. It is a simple activity that enriches our knowledge about digital content, and has gained popularity with services such as Del.icio. us. Del.icio. us has a large repository that evolves daily, presenting interesting new problems for IR. We present TagScore, a scoring function to rate the goodness of Del.icio. us tags for their associated web page. It gives us a succinct synopsis for a page that we can use to efficiently find similar pages. Using real Del.icio. us data, we show that our approach gives good correlation to cosine similarity but is several hundred times faster and requires minimal storage overhead.
Neuroeconomics, Naturalism, and Language

Neuroeconomics stays in the center of the ongoing naturalistic turn in economics. It portrays the individual as a complex system of decision making mechanisms and modules. This results into a conceptual tension with the standard economic notion of the unity of the actor that is a systemic property of economic coordination. I propose to supplement neuroeconomics with a naturalistic theory of social coordination. Recent neurobiological and psychological research strongly supports claims made by some heterodox economists that the identity of actors emerges from social interaction, especially in the context of the use of language. Therefore, I argue that the completion of the neuroeconomic paradigm requires a naturalistic theory of language. I provide some sketches based on teleosemantics and memetics, and exemplify the argument by a naturalist account of money.