Miracle-dz/UniFAR-FTUs huggingface dataset:
Ubiquitin pathway involvement in human lymphocyte gamma-irradiation-induced apoptosis

Apoptosis (the classical type of programmed cell death) can be triggered in many cell types by widely diverse stimuli. gamma rays, at low doses, can induce apoptosis in vitro in interphase human lymphocytes. In this type of apoptosis induction, activated gene expression is necessary for the fulfillment of the death program. In this report, we present evidence for a relationship between ubiquitin gene expression or ubiquitination and gamma-irradiation-mediated apoptosis in normal circulating human lymphocytes. Using in vitro nuclear transcription assays (run-on), Northern (RNA) blot analysis, immunolocalization studies, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis after immunoprecipitation, we demonstrate that (i) the ubiquitin mRNA level is increased as a consequence of the activation of ubiquitin gene transcription 15 to 90 min after initiation of apoptosis; (ii) specifically in apoptotic cells, and not in all irradiated cells, nuclear proteins are highly ubiquitinated; and (iii) ubiquitin sequence-specific antisense oligonucleotide inhibition results in a decreased level of ubiquitinated nuclear proteins and considerably diminishes the proportion of cells exhibiting the apoptotic death pattern. Each of these results might be explained by different modifications occurring in irradiated cells. Their convergence strongly suggests that the ubiquitin gene is one of the genes with induced activity in the apoptotic death program and that ubiquitination of nuclear proteins might be involved in chromatin disorganization and oligonucleosomal fragmentation, which are among the key events occurring in apoptosis.
Modeling the Physical Nexus across Water Supply, Wastewater Management and Hydropower Generation Sectors in River–Reservoir Systems

Most water supply and hydropower generation is obtained from the river–reservoir system, and wastewater pollutants are also dumped into the system. Increasing water demand and consumption have caused the water supply, wastewater pollutant management and hydropower generation sectors to be interlinked and to reinforce each other in the system. A physical nexus across water supply, wastewater management and hydropower generation sectors for a river–reservoir system was developed based on the analytical water quality and hydropower generation equations. Considering the Jinghong hydropower reservoir, located in the middle and lower reaches of the Lancangjiang River Basin, as a case study, both the wastewater pollutant management target and water inflow from the upstream as the external and boundary conditions, were employed to establish the effects of the external and boundary conditions on the nexus. It was demonstrated that the nexus of water supply and hydropower generation sectors does not vary with the water quality indicators and its protection target, without the separation of environmental flow in hydropower generation flow. In addition, the amount of hydropower generation decreases with increasing water supply. However, the lapse rates of allowable wastewater pollutants–water supply differ based on the water inflow and the wastewater pollutant management sectors, while the efficiency of hydropower generation and the sensitivity of allowable wastewater pollutants per amount of water supply are considered to be unrelated to the water inflow and wastewater pollutant management target conditions. The quantitative nexus developed through the proposed equation not only contributes to a more complete understanding of the mechanism of cross-connections, but also in creation of specific water protection and utilization measures, which is also the focus of the water–energy nexus.
Risk factors for irritable bowel syndrome: role of analgesics and food sensitivities

OBJECTIVE:Symptoms of irritable bowel syndrome (IBS) are reported by 10% of the general population; however, evaluation of traditional risk factors has not provided any insight into the pathogenesis of this condition. The objective of this study was to identify additional risk factors for irritable bowel syndrome.METHODS:A valid self-report questionnaire that records the gastrointestinal (GI) symptoms required for a diagnosis of IBS, self-reported measures of potential risk factors, and a psychosomatic symptom checklist was mailed to an age- and gender-stratified random sample of Olmsted County, Minnesota residents aged 30–64 yr. A logistic regression model that adjusted for age, gender, and psychosomatic symptom score was used to identify factors significantly associated with IBS.RESULTS:A total of 643 (72%) of 892 eligible subjects returned the survey. IBS symptoms were reported by 12% of the respondents. IBS was significantly associated with use of analgesics (acetaminophen, aspirin, or nonaspirin nonsteroidal antiinflammatory drugs) for reasons other than IBS, reporting a food allergy or sensitivity, and ratings of somatic symptoms. No association was detected for age, gender, body mass index, smoking history, alcohol use, educational level, exposure to pets in the household, or water supply. Among subjects reporting the use of just one type of analgesic, IBS was associated with acetaminophen but not aspirin or nonaspirin nonsteroidal antiinflammatory drugs used alone. The odds of having IBS were higher among subjects reporting more reasons for taking analgesics and intolerance to a higher number of foods.CONCLUSIONS:IBS is significantly associated with analgesic use. However, this is confounded by other somatic pain complaints. IBS symptoms are associated with the reporting of many food allergies or sensitivities. The role of food-induced symptoms in IBS requires further investigation.
A robust test of warm glow giving and spiteful pleasure in a â€œreal donationâ€ experiment with and without earned endowments

Behavioral research provides evidence consistent with individuals enjoying kind acts (Crumpler and Grossman, 2008) and with individuals enjoying harmful acts (Abbink and Herrmann, 2011). This paper reports on an experiment designed to test if kind or harmful acts are an artefact of the experimental design. We investigate this question using a â€œreal donationâ€ laboratory experiment (Eckel and Grossman 1996) in which participants make a dictator allocation decision and are paired with an actual charity. We use a 2x3 design to vary the action set (only give to charity, or, give to or take from charity) and the source of the endowment (house money, earned endowment, or earned charity endowment). The experiment is designed so that a pure altruist has no incentive to donate or take. In the context of the â€œreal donationâ€ experiment, we observe very few participants taking money from charity. We find that giving persists when the endowment is earned, and when participants are given the option to take. The results are consistent with a warm glow motivation for giving.
Trial pruning for classification of single-trial EEG data during motor imagery

Due to the artifacts in electroencephalography (EEG) data, the performance of brain-computer interface (BCI) is degraded. On the other hand, in the motor imagery based BCI system, EEG signals are usually contaminated by the misleading trials caused by improper imagination of a movement. In this paper, we present a novel algorithm to detect the abnormal EEG data using genetic algorithm (GA). After trial pruning, a subset of the EEG data are selected, on which common spatial pattern (CSP) and Gaussian classifier are trained. The performance of the proposed method is tested on Data set IIa of BCI Competition IV, and the simulation result demonstrates a significant improvement for six out of nine subjects.
China's Censorship 2.0: How Companies Censor Bloggers

This study explores an under-studied layer of Chinese Internet censorship: how Chinese Internet companies censor user-generated content, usually by deleting it or preventing its publication. Systematic testing of Chinese blog service providers reveals that domestic censorship is very decentralized with wide variation from company to company. Test results also showed that a great deal of politically sensitive material survives in the Chinese blogosphere, and that chances for its survival can likely be improved with knowledge and strategy. The study concludes that choices and actions by private individuals and companies can have a significant impact on the overall balance of freedom and control in the Chinese blogosphere.
ISG15 Deregulates Autophagy in Genotoxin-treated Ataxia Telangiectasia Cells*

Background: Aberrant activation of autophagy (proteinopathy) leads to neurodegeneration in various neurological disorders. Results: Compensatory basal autophagy is activated, and genotoxins deregulate autophagy in the ubiquitin pathway-compromised ataxia telangiectasia (A-T) cells. Conclusion: Deregulation of autophagy is due to the elevated expression of ISG15 in A-T cells. Significance: Results highlight a causal contribution of a novel “ISG15 proteinopathy” in A-T neurodegeneration. Ataxia-telangiectasia (A-T) is a cerebellar neurodegenerative disorder; however, the basis for the neurodegeneration in A-T is not well established. Lesions in the ubiquitin and autophagy pathways are speculated to contribute to the neurodegeneration in other neurological diseases and may have a role in A-T neurodegeneration. Our recent studies revealed that the constitutively elevated ISG15 pathway impairs targeted proteasome-mediated protein degradation in A-T cells. Here, we demonstrate that the basal autophagy pathway is activated in the ubiquitin pathway-compromised A-T cells. We also show that genotoxic stress triggers aberrant degradation of the proteasome and autophagy substrates (autophagic flux) in A-T cells. Inhibition of autophagy at an early stage using 3-methyladenine blocked UV-induced autophagic flux in A-T cells. On the other hand, bafilomycin A1, which inhibits autophagy at a late stage, failed to block UV-induced autophagic flux, suggesting that overinduction of autophagy may underlie aberrant autophagic flux in A-T cells. The ISG15-specific shRNA that restored proteasome function restores autophagic function in A-T cells. These findings suggest that autophagy compensates for the ISG15-dependent ablation of proteasome-mediated protein degradation in A-T cells. Genotoxic stress overactivates this compensatory mechanism, triggering aberrant autophagic flux in A-T cells. Supporting the model, we show that autophagy is activated in the brain tissues of human A-T patients. This highlights a plausible causal contribution of a novel “ISG15 proteinopathy” in A-T neuronal cell death.
From "Overview" to "Detail": An Exploration of Contextual Transparency for Public Transparent Interfaces

This study explores the contextual transparency of information presented on public transparent user interfaces through the maintenance of adequate legibility. To address this issue, we investigate the relationship between the information and transparency in a shop context. In this paper, we present an experiment which examines the effects of transparency, changing user's proximity, and information types on legibility with a public transparent information system. We report significant effects on performance and legibility, and the results indicate the different contextual transparency related to the user's proximity, depending on whether the user focuses on the information or the environment. In addition, under the 50% transparency (25% and 50% levels) fit into the closer proximity while the 50% transparency offers more harmonious view in a distant context. The implications of these results to the usability of public transparent user interfaces and design recommendations are also discussed.
On the verification of intransitive noninterference in mulitlevel security

We propose an algorithmic approach to the problem of verification of the property of intransitive noninterference (INI), using tools and concepts of discrete event systems (DES). INI can be used to characterize and solve several important security problems in multilevel security systems. In a previous work, we have established the notion of iP-observability, which precisely captures the property of INI. We have also developed an algorithm for checking iP-observability by indirectly checking P-observability for systems with at most three security levels. In this paper, we generalize the results for systems with any finite number of security levels by developing a direct method for checking iP-observability, based on an insightful observation that the iP function is a left congruence in terms of relations on formal languages. To demonstrate the applicability of our approach, we propose a formal method to detect denial of service vulnerabilities in security protocols based on INI. This method is illustrated using the TCP/IP protocol. The work extends the theory of supervisory control of DES to a new application domain.
Socioeconomic status over the life course and allostatic load in adulthood: results from the Northern Swedish Cohort

Background Although several studies have reported rather consistent associations between socioeconomic status (SES) and allostatic load (AL), so far no study has examined the influence of SES over the life course on AL. The aim of the present study was to investigate the association between SES over the life course and AL in mid-adulthood, guided by the conceptual models of cumulative risk, critical period and social chain of risk. Methods The sample comprises a 27-year prospective cohort (n=1071) from northern Sweden. Participants (n=855, 79.8%) completed questionnaires at the ages of 16, 21, 30 and 43 years. A health examination was performed at age 43 years after an overnight fast, including physical examination and blood sampling, and participants completed 1-day salivary cortisol sampling (four samples). SES was based on parental occupation at age 16 years and participants' own occupation at ages 21, 30 and 43 years. Information on daily smoking, snuff use, high alcohol consumption and physical inactivity was reported by the participants. An AL index was constructed from tertiles of 12 biological parameters. Results Cumulative socioeconomic disadvantage was related to AL in both women and men. The association was largely explained by health behaviours in men, but was independent of health behaviours in women. In women, an association was observed between AL and SES in adolescence, whereas in men only current SES was related to AL, independently of current health behaviours. Conclusions SES over the life course influences the level of multi-systemic dysregulation in mid-adulthood, with the strongest support for the cumulative risk model.
Timed Default Concurrent Constraint Programming

Abstract Synchronous programming (Berry, 1989) is a powerful approach to programming reactive systems. Following the idea that “processes are relations extended over time” (Abramsky, 1993), we propose a simple but powerful model for timed, determinate computation, extending the closure-operator model for untimed concurrent constraint programming (CCP). In Saraswat et al . (1994a) we had proposed a model for this called tcc—here we extend the model of tcc to express strong time-outs: if an event A does not happen through time t , cause event B to happen at time t . Such constructs arise naturally in practice (e.g. in modeling transistors) and are supported in synchronous programming languages. The fundamental conceptual difficulty posed by these operations is that they are non-monotonic. We provide compositional semantics to the non-monotonic version of concurrent constraint programming (Default cc) obtained by changing the underlying logic from intuitionistic logic to Reiter's default logic. This allows us to use the same construction (uniform extension through time) to develop Default cc as we had used to develop tcc from cc. Indeed the smooth embedding of cc processes into Default cc processes lifts to a smooth embedding of tcc processes into Default cc processes. We identify a basic set of combinators (that constitute the Default cc programming framework), and provide constructive operational semantics (implemented by us as an interpreter) for which the model is fully abstract. We show that the model is expressive by defining combinators from the synchronous languages. We show that Default cc is compositional and supports the properties of multiform time, orthogonal pre-emption and executable specifications. In addition, Default cc programs can be read as logical formulae (in an intuitionistic temporal logic)—we show that this logic is sound and complete for reasoning about (in)equivalence of Default cc programs. Like the synchronous languages, Default cc programs can be compiled into finite state automata. In addition, the translation can be specified compositionally. This enables separate compilation of Default cc programs and run-time tradeoffs between partial compilation and interpretation. A preliminary version of this paper was published as Saraswat et al . (1995). Here we present a complete treatment of hiding, along with a detailed treatment of the model.
Measuring Similarity of Elements in OWL DL Ontologies

OWL becomes nowadays a more and more widely-used language for representing ontologies. The number of OWL ontologies increasing in direct ratio to the development of the Semantic Web leads to the heterogeneity problem. The same concepts may be modeled differently, using different terms and different positions in concept hierarchy. The task of identifying similar entities (concepts, relations or individuals) in different ontologies becomes then crucial for the success of information integration systems, instance transformation. In this paper, we propose a new similarity measure for comparing entities in different OWL DL ontologies. This measure is designed so as to enable extraction of information encoded in OWL entity descriptions and to take into account the underlying meaning of OWL primitives. We propose a variable weighting scheme for combining more efficiently component similarities calculated from components in entity descriptions.
Pitch-Tracking of Reverberant Sounds, Application to Spatial Description of Sound Scenes

Fundamental frequency (F0) is useful as a perceptually-relevant sound descriptor, and also as an ingredient for signal processing applied to analysis of sound scenes. Here, a recently proposed multiple-F0 algorithm is adapted to handle reverberation in monophonic or multichannel recordings; the information that is obtained from it is then applied to estimation of reverberation time from recorded musical signals.
Spanning trees on graphs and lattices in d dimensions

The problem of enumerating spanning trees on graphs and lattices is considered. We obtain bounds on the number of spanning trees NST and establish inequalities relating the numbers of spanning trees of different graphs or lattices. A general formulation is presented for the enumeration of spanning trees on lattices in d≥2 dimensions, and is applied to the hypercubic, body-centred cubic, face-centred cubic and specific planar lattices including the kagome, diced, 4-8-8 (bathroom-tile), Union Jack and 3-12-12 lattices. This leads to closed-form expressions for NST for these lattices of finite sizes. We prove a theorem concerning the classes of graphs and lattices with the property that NST~exp (nz) as the number of vertices n→∞, where z is a finite non-zero constant. This includes the bulk limit of lattices in any spatial dimension, and also sections of lattices whose lengths in some dimensions go to infinity while others are finite. We evaluate z exactly for the lattices we consider, and discuss the dependence of z on d and the lattice coordination number. We also establish a relation connecting z to the free energy of the critical Ising model for planar lattices.
Evolutionary emergence of responsive and unresponsive personalities

In many animal species, individuals differ consistently in suites of correlated behaviors, comparable with human personalities. Increasing evidence suggests that one of the fundamental factors structuring personality differences is the responsiveness of individuals to environmental stimuli. Whereas some individuals tend to be highly responsive to such stimuli, others are unresponsive and show routine-like behaviors. Much research has focused on the proximate causes of these differences but little is known about their evolutionary origin. Here, we provide an evolutionary explanation. We develop a simple but general evolutionary model that is based on two key ingredients. First, the benefits of responsiveness are frequency-dependent; that is, being responsive is advantageous when rare but disadvantageous when common. This explains why responsive and unresponsive individuals can coexist within a population. Second, positive-feedback mechanisms reduce the costs of responsiveness; that is, responsiveness is less costly for individuals that have been responsive before. This explains why individuals differ consistently in their responsiveness, across contexts and over time. As a result, natural selection gives rise to stable individual differences in responsiveness. Whereas some individuals respond to environmental stimuli in all kinds of contexts, others consistently neglect such stimuli. Interestingly, such differences induce correlations among all kinds of other traits (e.g., boldness and aggressiveness), thus providing an explanation for environment-specific behavioral syndromes.
Assessing the Suitability of the Chilbolton Radars for Space Debris and Space Surveillance Applications

The Science and Technology Facilities Council (STFC) operates several radars installed on its fully-steerable 25-metre diameter dish antenna at the Chilbolton Observatory in southern England. In the past, these radars have successfully detected a variety of satellite targets. High range resolution (HRR) radar profiling of ground-based targets has also been conducted. Recently, as part of the in-orbit testing activity for the EU μ*DOLOHR¶ SURJUDPPH WKe Chilbolton antenna has demonstrated highly accurate satellite tracking. This combination of satellite detection, HRR radar profiling and high-fidelity antenna tracking represents a useful capability for space debris and space surveillance work. Here, we describe the Chilbolton site, the 25-metre dish, its radars, and the results obtained in past experiments. Plans for future Space Situational Awareness (SSA)related work at Chilbolton Observatory are outlined. The potential for Chilbolton, and other STFC assets, to contribute to the radar element of a European SSA network is discussed.
Efficient use of the BlobTree for rendering purposes

One of the major applications of implicit surface modeling systems has been the generation of cartoon-like characters. Recently, additional modeling methods have been combined with implicit surfaces to create much more complex models. These methods include constructive solid geometry (CSG), warping, and two-dimensional texture mapping (among others). The BlobTree has been introduced to organize all of these elements into a single structure which allows both local and global applications of each of these techniques in a general and intuitive fashion. The BlobTree lends itself well to rapid and direct specification of complex models, however current implementations of the BlobTree have not been engineered for efficiency, and perform poorly when attempting to render large models. In this work we apply established techniques, such as spatial subdivision and tree optimization, to the BlobTree. The objective is to increase efficiency during rendering without restricting the functionality of the BlobTree as a modeling tool.