Miracle-dz/UniFAR-FTUs huggingface dataset:
G-quadruplexes in promoters throughout the human genome

Certain G-rich DNA sequences readily form four-stranded structures called G-quadruplexes. These sequence motifs are located in telomeres as a repeated unit, and elsewhere in the genome, where their function is currently unknown. It has been proposed that G-quadruplexes may be directly involved in gene regulation at the level of transcription. In support of this hypothesis, we show that the promoter regions (1 kb upstream of the transcription start site TSS) of genes are significantly enriched in quadruplex motifs relative to the rest of the genome, with >40% of human gene promoters containing one or more quadruplex motif. Furthermore, these promoter quadruplexes strongly associate with nuclease hypersensitive sites identified throughout the genome via biochemical measurement. Regions of the human genome that are both nuclease hypersensitive and within promoters show a remarkable (230-fold) enrichment of quadruplex elements, compared to the rest of the genome. These quadruplex motifs identified in promoter regions also show an interesting structural bias towards more stable forms. These observations support the proposal that promoter G-quadruplexes are directly involved in the regulation of gene expression.
Measuring Socioeconomic Status at Individual and Collective Levels

This study investigated the multilevel dimensionality of socioeconomic status and its relationship to reading achievement in 23 countries. Different factor structures of SES were found at different levels’ observations and in different countries. The study showed that the cultural dimension strongly related to student reading performance, while the school general capital dimension explained a large part of the between-school reading achievement differences. Most interestingly, the factor relationship between SES and reading achievement at the school level varies greatly across countries. It was argued that these variations might be due to the differences in the centralized versus decentralized educational finance, tracking mechanism and some social characteristics in different countries.
Insights on the Emergence of Mycobacterium tuberculosis from the Analysis of Mycobacterium kansasii

By phylogenetic analysis, Mycobacterium kansasii is closely related to Mycobacterium tuberculosis. Yet, although both organisms cause pulmonary disease, M. tuberculosis is a global health menace, whereas M. kansasii is an opportunistic pathogen. To illuminate the differences between these organisms, we have sequenced the genome of M. kansasii ATCC 12478 and its plasmid (pMK12478) and conducted side-by-side in vitro and in vivo investigations of these two organisms. The M. kansasii genome is 6,432,277 bp, more than 2 Mb longer than that of M. tuberculosis H37Rv, and the plasmid contains 144,951 bp. Pairwise comparisons reveal conserved and discordant genes and genomic regions. A notable example of genomic conservation is the virulence locus ESX-1, which is intact and functional in the low-virulence M. kansasii, potentially mediating phagosomal disruption. Differences between these organisms include a decreased predicted metabolic capacity, an increased proportion of toxin–antitoxin genes, and the acquisition of M. tuberculosis-specific genes in the pathogen since their common ancestor. Consistent with their distinct epidemiologic profiles, following infection of C57BL/6 mice, M. kansasii counts increased by less than 10-fold over 6 weeks, whereas M. tuberculosis counts increased by over 10,000-fold in just 3 weeks. Together, these data suggest that M. kansasii can serve as an image of the environmental ancestor of M. tuberculosis before its emergence as a professional pathogen, and can be used as a model organism to study the switch from an environmental opportunistic pathogen to a professional host-restricted pathogen.
Seeing is retrieving: building information context from what the user sees

As the user's document and application workspace grows more diverse, supporting personal information management becomes increasingly important. This trend toward diversity renders it difficult to implement systems which are tailored to specific applications, file types, or other information sources. We developed SeeTrieve, a personal document retrieval and classification system which abstracts applications by considering only the text they present to the user through the user interface. Associating the visible text which surrounds a document in time, SeeTrieve is able to identify important information about the task within which a document is used. This context enables novel, useful ways for users to retrieve their personal documents. When compared to content based systems, this context based retrieval achieved substantial improvements in document recall.
Millennial Capitalism and the Culture of Neoliberalism

The essays in Millennial Capitalism and the Culture of Neoliberalism pose a series of related questions: How are we to understand capitalism at the millennium? Is it a singular or polythetic creature? What are we to make of the culture of neoliberalism that appears to accompany it, taking on simultaneously local and translocal forms? To what extent does it make sense to describe the present juncture in world history as an “age of revolution,” one not unlike 1789–1848 in its transformative potential? In exploring the material and cultural dimensions of the Age of Millennial Capitalism, the contributors interrogate the so-called crisis of the nation-state, how the triumph of the free market obscures rising tides of violence and cultures of exclusion, and the growth of new forms of identity politics. The collection also investigates the tendency of neoliberal capitalism to produce a world of increasing differences in wealth, environmental catastrophes, heightened flows of people and value across space and time, moral panics and social impossibilities, bitter generational antagonisms and gender conflicts, invisible class distinction, and “pariah” forms of economic activity. In the process, the volume opens up an empirically grounded, conceptual discussion about the world-at-large at a particularly momentous historical time—when the social sciences and humanities are in danger of ceding intellectual initiative to the masters of the market and the media. In addition to its crossdisciplinary essays, Millennial Capitalism and the Culture of Neoliberalism— originally the third installment of the journal Public Culture ’s “Millennial Quartet”—features several photographic essays. The book will interest anthropologists, political geographers, economists, sociologists, and political theorists. Contributors. Scott Bradwell, Jean Comaroff, John L. Comaroff, Fernando Coronil, Peter Geschiere, David Harvey, Luiz Paulo Lima, Caitrin Lynch, Rosalind C. Morris, David G. Nicholls, Francis Nyamnjoh, Elizabeth A. Povinelli, Paul Ryer, Allan Sekula, Irene Stengs, Michael Storper, Seamus Walsh, Robert P. Weller, Hylton White, Melissa W. Wright, Jeffrey A. Zimmerman
Asylum seekers: How attributions and emotion affect Australians' views on mandatory detention of “the other”

There is little research regarding the social psychological processes shaping community opinions about asylum seeker policy. Here, we explored two issues by way of a random community survey of the Perth metropolitan area. We first examined whether the intergroup perceptions that occur when individuals focus upon the Australian community (self-focus) or asylum seekers themselves (other-focus) when evaluating the issue of asylum seekers in detention affected community opinions. Regarding self-focus, perceiving the Australian community as stable (not seeing asylum seekers as a threat to the stability of Australian society) predicted a more lenient policy orientation, as did perceiving the government's policy as illegitimate. Regarding other-focus, perceiving asylum seekers as legitimate, their situation in detention as unstable, and empathy predicted a more lenient policy orientation. Second, we examined the accuracy with which participants estimated wider community consensus for their respective policy orientation. As predicted, over-estimation increased as participants favoured tougher policy.
Optimization of the dose of intrathecal morphine in total hip surgery: a dose-finding study.

UNLABELLED We designed this study to determine the optimal intrathecal dose of morphine in total hip surgery. The optimal intrathecal dose was defined as that providing effective analgesia and minimal side effects 24 h after total hip surgery. Patients (n = 143) scheduled for total hip surgery were randomized to four double-blinded groups with a standardized bupivacaine dose but different doses of intrathecal morphine (Group I = 0.025 mg, Group II = 0.05 mg, Group III = 0.1 mg, and Group IV = 0.2 mg). Pain scores, i.v. morphine intake (patient-controlled analgesia), and morphine-related side effects (respiratory depression, postoperative nausea and vomiting, itching, urinary retention) were recorded for 24 h after surgery. Excellent postoperative pain relief was present in all groups. The highest pain scores were found in Group I. The mean use of systemic morphine administered by patient-controlled analgesia infusion pump was 23.7, 17.8, 10.9, and 9.9 mg in Groups I-IV, respectively (P < 0.01 for Groups III and IV versus Group I). We conclude that 0.1 mg of intrathecal morphine is the optimal dose for pain relief after hip surgery with minimal side effects. IMPLICATIONS Earlier studies showed excellent postoperative pain relief after intrathecal morphine. However, the severity of side effects resulted in decreased enthusiasm for this anesthesia technique. In the present study, we show that an intrathecal dose of 0.1 mg of morphine can be used safely in total hip surgery with excellent postoperative pain relief.
Introduction to a special session on EMC and information security

This paper introduces the special section on EMC and Information Security. As information security becomes more important every day, safeguarding security at the physical level is as important as at the higher levels. In recent years, instrumentation has become cheaper and more precise, computation has become faster, and storage capacity has increased. With these changes, the threat has increased of advanced attacks that were previously too difficult to carry out, not just in the military and diplomatic fields but also for general-use commercial manufactured goods. This special session focuses on the problem of reduced security concerning electromagnetic waves (electromagnetic information security), which has made attack detection particularly difficult at the physical level. As well as introducing the mechanisms of these information leaks and countermeasures, this session presents the latest research trends.
How is the indoor environment related to asthma?: literature review.

AIMS This paper reports a review conducted to identify the factors in the indoor environment that have an evidence-based link with the exacerbation or development of asthma and to identify measures that healthcare professionals can promote to reduce exposure to these risk factors in the home. BACKGROUND The indoor environment, particularly at home, has been recognized as a major source of exposure to allergens and toxic chemicals. Exposure to allergens and toxins is thought to exacerbate respiratory conditions, in particular, asthma. METHODS Searches were made of health and indoor environment databases, including Cochrane Library, National Health Services Centre for Reviews and Assessment Reports, British Medical Journal, CINAHL and Ovid library, MEDSCAPE/MEDLINE, EMBASE, INGENTA, Science Citation Index, Web of Science. Searches were also made of other Internet-based resources, including those of international and government bodies. The following keywords were used: allergens, allergen avoidance, asthma, asthma prevention, cat, damp, Der p 1, dog, environmental control, house dust mites, indoor air quality, indoor environment, meta analysis, mould, pets, remedial actions, respiratory illnesses and systematic reviews. FINDINGS There is evidence of a link between asthma and a small number of indoor environmental factors. There is currently only reasonable evidence for one causative factor for asthma in the indoor environment and that is house dust mite allergen. Although there are many studies of different remedial actions that can be taken in the home, often these give evidence of reduced risk of exposure but not clinical improvement in asthma. Although there is a lack of medical evidence for the reduction of known sensitizers such as mould, this is because of a dearth of research rather than evidence of no association. CONCLUSIONS There is some evidence of a link between the indoor environment and asthma. There are measures, which could be promoted by healthcare professionals to alleviate asthmatic symptoms.
Paper Introduction of Economic-oriented Fairness to Process Al- Gebras

Fairness is one of the important notion for programming language, such as process algebras like CCS, that includes concurrency (or parallelism) and nondeterminism . This ensures that while repeatedly choosing among a set of alternatives, no alternative will be postponed forever. However, the fairness does not mention at what frequency these alternatives are selected. In this paper, we propose a quantitative fairness, which is called economic-oriented fairness, to each alternatives. This fairness ensures that the expected number of selection for each alternatives are same. We give a condition for probability assignment of selection of each alternative to be satis ed for economic-oriented fairness. First we show a simple probability assignment rule. In this assignment, between any two alternatives, if an alternative is selected n times and the other m times then the probability to select the former alternative is (m + 1)=(n + 1) times the probability for the latter. We prove that this assignment satis es the condition of economic-oriented fairness. For a model of the economic-oriented fairness, we adopt a probabilistic process algebra. Finally, we elaborate with two process models of the economic-oriented fairness. The rst one is a server and client model, where each client communicates only with the server, but not among them. In this model, the expected number of communication by each client are equal. The second model considers communication between two processes. In practice, a process has several subprocesses. Each subprocess communicates via a communication port. In the second model, there is economic-oriented fairness where the expected number of communications via each communication port are equal. key words: fairness, economic-oriented fairness, process algebra, CCS
CodY Is a Nutritional Repressor of Flagellar Gene Expression in Bacillus subtilis

ABSTRACT Expression of the σD-dependent flagellin gene, hag, is repressed by the CodY protein in nutrient-rich environments. Analysis of a codY mutant bearing a hag-lacZ reporter suggests that the availability of amino acids in the environment is the specific signal that triggers this repression. Further, hag-lacZ expression appears to be sensitive to intracellular GTP levels, as demonstrated by increased expression upon addition of decoyinine. This result is consistent with the postulate that the availability of amino acids in the environment effects intracellular GTP levels through the stringent response. However, the levels of hag-lacZ measured upon the addition of subsets of amino acids suggest an additional mechanism(s). CodY is a DNA binding protein that could repress flagellin expression directly by binding to the hag promoter region, or indirectly by binding to the fla/che promoter region that governs expression of the σD transcriptional activator required for hag gene expression. Using an electrophoretic mobility shift assay, we have demonstrated that purified CodY protein binds specifically to both the hag and fla/che promoter fragments. Additionally, CodY acts as a nutritional repressor of transcription from the fla/che promoter region that contains two functional promoters. CodY binds to both the σD- and σA-dependent promoters in this region, as demonstrated by DNase I footprint analyses. Footprint analyses of the hag gene demonstrated that CodY binds downstream of its σD-dependent promoter. Taken together, these results identify new members of the CodY regulon that encode motility functions in Bacillus subtilis and are controlled by the σD alternate sigma factor.
Dynamic Coding of Signed Quantities in Cortical Feedback Circuits

In the early sensory and motor areas of the cortex, individual neurons transmit information about specific sensory features via a peaked response. This concept has been crystallized as “labeled lines,” to denote that axons communicate the specific properties of their sensory or motor parent cell. Such cells also can be characterized as being polarized, that is, as representing a signed quantity that is either positive or negative. We show in a model simulation that there are two important consequences when learning receptive fields using such signed codings in circuits that subtract different inputs. The first is that, in feedback circuits using labeled lines, such arithmetic operations need to be distributed across multiple distinct pathways. The second consequence is that such pathways must be necessarily dynamic, i.e., that synapses can grow and retract when forming receptive fields. The model monitors the breaking and growing of new circuit connections when their synapses need to change polarities and predicts that the rate of such changes should be inversely correlated with the progress of receptive field formation.
Visual attitude control using a virtual barycenter of a quadrangle that constructed from feature points for outdoor autonomous mobile robots

We proposed a visual attitude control for an outdoor autonomous mobile robot. The attitude control method uses a virtual barycenter of the quadrangle that is constructed from four feature points in camera image. By tracking four feature points using optical flow at all time, the quadrangle is updated using the same feature points, and its virtual barycenter is calculated. The quadrangle maintains the similar figure during a robot's movement. Therefore, its virtual barycenter stays at the same position when the mobile robot moves straight. On the other hand, the position of the virtual barycenter varies in proportion to the movement in the horizontal direction of the mobile robot. We demonstrated that the autonomous mobile robot equipped with this visual attitude control was able to move exactly between way points. The experimental results proved that the visual attitude control is useful for mobile robots.
pigenetic mechanisms in human adenovirus type 12 oncogenesis

For the past 30 years, my laboratory has concentrated its work on demonstrating that the epigenetic consequences of foreign DNA insertion into established mammalian genomes – de novo DNA methylation of the integrate and alterations of methylation patterns across the recipient genome – are essential elements in setting the stage towards oncogenic transformation. We have primarily studied human adenovirus type 12 (Ad12) which induces undifferentiated tumors in Syrian hamsters (Mesocricetus auratus) either at the site of subcutaneous Ad12 injection or intraperitoneally upon intramuscular injection. Up to
Isolation and characterization of dental pulp stem cells from a supernumerary tooth.

BACKGROUND Dental pulp stem cells (DPSCs) were primarily derived from the pulp tissues of primary incisors and permanent third molar teeth, whereas no report to our knowledge has yet been documented on deriving DPSCs from the other tooth types. The aim of this study is to present a novel approach of harvesting stem cells from a supernumerary tooth (a mesiodens). MATERIALS AND METHODS The pulp tissues from a mesiodens of a 20-year-old healthy male patient and the left lower deciduous canine of a healthy 10-year-old boy (the positive control) were extracted and cultured for DPSCs, which were examined with stem cells (Oct-4, Nanog and Rex-1) and differentiation (Osteonectin and Nestin) markers. Furthermore, DPSCs were directionally differentiated to osteogenic and adipogenic cell lineages. RESULTS Dental pulp stem cells derived from the mesiodens were capable of differentiating into adipogenic and osteogenic lineages. The mesioden's DPSCs also expressed stem cell and differentiation markers, which suggested their stem cell origin and differentiation capability. All the aforementioned results for the mesiodens were consistent with those of the DPSCs derived from the positive control. CONCLUSION We have demonstrated the feasibility of deriving DPSCs from a usually discarded tissue such as a supernumerary tooth.
Patterns of Distress in African-American Mothers of Preterm Infants

Objective: To examine inter-relationships among stress due to infant appearance and behavior in the neonatal intensive care unit (NICU), parental role alteration stress in the NICU, depressive symptoms, state anxiety, posttraumatic stress symptoms, and daily hassles exhibited by African-American mothers of preterm infants and to determine whether there were subgroups of mothers based on patterns of psychological distress. Method: One hundred seventy-seven African-American mothers completed questionnaires on their psychological distress at enrollment during infant hospitalization and 2, 6, 12, 18, and 24 months after term. Results: Psychological distress measures were intercorrelated. There were four latent classes of mothers: the low distress class with low scores on all measures; the high NICU-related stress class with high infant appearance and parental role stress and moderate scores on other measures; the high depressive symptoms class with high depressive symptoms and state anxiety and moderately elevated scores on NICU-related stress and posttraumatic stress symptoms; the extreme distress class with the highest means on all measures. Infants in the high stress class were sicker than infants in the other classes. The extreme distress class mothers averaged the lowest educational level. The classes differed on distress measures, worry about the child, and parenting stress through 24 months with the extreme distress class having the highest values. Conclusion: Although different types of maternal psychological distress were substantially related, there were distinct subgroups of mothers that were identifiable in the NICU. Moreover, these subgroups continued to differ on trajectories of distress and on their perceptions of the infants and parenting through 24 months after term.