Miracle-dz/UniFAR-FTUs huggingface dataset:
Up‐regulation of the SOX3 gene expression by retinoic acid: characterization of the novel promoter‐response element and the retinoid receptors involved

Sox3/SOX3 gene is considered to be one of the earliest neural markers in vertebrates and it is implicated in the genetic cascades that direct brain formation. We have previously shown that early phases of differentiation and neural induction of NT2/D1 embryonal carcinoma cells by retinoic acid (RA) involve up‐regulation of the SOX3 gene expression. Here, we present identification of a novel positive regulatory promoter element involved in RA‐dependent activation of the SOX3 gene expression in NT2/D1 cells. This element represents a direct repeat 3‐like motif that directly interacts with retinoid X receptor (RXR) α in a sequence‐specific manner. It is capable of independently mediating the RA effect in a heterologous promoter context and its disruption caused significant reduction of RA/RXR transactivation of the SOX3 promoter. Furthermore, by using synthetic antagonists of retinoid receptors, we have shown for the first time, that RA‐induced SOX3 gene expression could be significantly down‐regulated by the synthetic antagonist of RXR. Also, this data showed that RXRs, but not RA receptors, are mediators of RA effect on the SOX3 gene up‐regulation in NT2/D1 cells. Presented data will be valuable for future investigation of SOX3 gene expression, not only in NT2/D1 model system, but also in diverse developmental, physiological and pathological settings.
Usefulness of a New Immunoradiometric Assay of HCV Core Antigen to Predict Virological Response during PEG-IFN/RBV Combination Therapy for Chronic Hepatitis with High Viral Load of Serum HCV RNA Genotype 1b

We investigated the clinical usefulness of a new immunoradiometric (IRM) assay of hepatitis C virus (HCV) core antigen in predicting virological response during pegylated interferon plus ribavirin (PEG-IFN/RBV) combination therapy for chronic hepatitis with high viral loads of serum HCV RNA genotype 1b. Thirty-nine patients received a regimen of PEG-IFNα-2b (1.5 µg/kg/week s.c.) in combination with RBV (600–1,000 mg/day). Of the 39 patients, 18 (46.2%) achieved sustained virological response (SVR), 11 (28.2%) attained partial response (PR) and 10 (25.6%) showed no response (NR). Four weeks after the start of therapy, 1- and 2-log reductions in the amount of HCV core antigen were observed in 20 (2/10) and 0% (0/10) showing NR, 91 (10/11) and 63.6% (7/11) with PRs, and 88.9 (16/18) and 55.6% (10/18) of patients with SVR, respectively. The 1- and 2-log reductions 4 weeks after the start of therapy were not a definingcondition for PR and SVR. The amount of HCV core antigen was significantly different between SVR and PR patients on days 1 and 7, and between patients with NR and SVR at all points of time. In conclusion, this new IRM assay is useful in predicting virological response during PEG-IFN/RBV therapy.
Optimizing cell decomposition path planning for mobile robots using different metrics

Many robot planning approaches use cell decomposition methods for finding a sequence of regions that the robot should traverse. When a fully-actuated robot is used, the robot reference trajectory is simply constructed by linking through line segments the middle points of common facets of successive traversed cells. This paper improves this approach by proposing three different optimizations that yield the waypoints through which the robot piecewise linear route is passing. The optimizations use different metrics defined as sums of norms for the linear segments that compose the route. The norms L1, L2 squared and L∞ are used and standard optimization problems result in each case. Examples are included for showing the usefulness of these optimizations, since shorter routes can be obtained under a negligible computational overhead.
Fifteen years after "Wingspread"--environmental endocrine disrupters and human and wildlife health: where we are today and where we need to go.

In 1991, a group of expert scientists at a Wingspread work session on endocrine-disrupting chemicals (EDCs) concluded that "Many compounds introduced into the environment by human activity are capable of disrupting the endocrine system of animals, including fish, wildlife, and humans. Endocrine disruption can be profound because of the crucial role hormones play in controlling development. " Since that time, there have been numerous documented examples of adverse effects of EDCs in invertebrates, fish, wildlife, domestic animals, and humans. Hormonal systems can be disrupted by numerous different anthropogenic chemicals including antiandrogens, androgens, estrogens, AhR agonists, inhibitors of steroid hormone synthesis, antithyroid substances, and retinoid agonists. In addition, pathways and targets for endocrine disruption extend beyond the traditional estrogen/androgen/thyroid receptor-mediated reproductive and developmental systems. For example, scientists have expressed concern about the potential role of EDCs in increasing trends in early puberty in girls, obesity and type II diabetes in the United States and other populations. New concerns include complex endocrine alterations induced by mixtures of chemicals, an issue broadened due to the growing awareness that EDCs present in the environment include a variety of potent human and veterinary pharmaceutical products, personal care products, nutraceuticals and phytosterols. In this review we (1) address what have we learned about the effects of EDCs on fish, wildlife, and human health, (2) discuss representative animal studies on (anti)androgens, estrogens and 2,3,7,8-tetrachlorodibenzo-p-dioxin-like chemicals, and (3) evaluate regulatory proposals being considered for screening and testing these chemicals.
Morphological and molecular characteristics of a poorly known marine ascomycete, Manglicola guatemalensis (Jahnulales: Pezizomycotina; Dothideomycetes, Incertae sedis): new lineage of marine ascomycetes

The poorly known marine ascomycete Manglicola guatemalensis from Trang and Trat provinces, Thailand, were collected in 2005 and 2006 on the brackish water palm Nypa fruticans. This fungus is known only from two previous collections. This paper reports on the morphological characteristics and molecular phylogeny of this unique marine bitunicate ascomycete. Manglicola guatemalensis has large clavate to obtusely fusiform ascomata, wide ostioles, bitunicate asci, cylindrical, thick-walled, unequally one-septate ascospores, constricted at the septum, apical cell larger, chestnut-brown and a smaller light brown basal cell. Ascospores germinate readily, always from the basal cell. Four isolates from different locations were selected for the phylogenetic study. Regions of the rDNA gene, including SSU and LSU, were sequenced and combined. Molecular data places M. guatemalensis in the Jahnulales with high bootstrap support; all strains are monophyletic. In the combined SSU and LSU analyses the Jahnulales comprises four subclades, A, B, C and D. Subclade A comprises Jahnula species and two anamorphic fungi, Brachiosphaera tropicalis and Xylomyces chlamydosporus. In subclade B Manglicola strains form a sister group of the Aliquandostipite species Aliquandostipite crystallinus, A. khaoyaiensis, Jahnula siamensiae and Patescospora separans. Subclade C comprises Jahnula species, Jahnula aquatica, J. granulosa and J. rostrata, while Megalohypha aqua-dulces constitutes subclade D. Therefore Manglicola forms another lineage of marine fungi.
Regulation of the JMJD3 (KDM6B) histone demethylase in glioblastoma stem cells by STAT3

The growth factor and cytokine regulated transcription factor STAT3 is required for the self-renewal of several stem cell types including tumor stem cells from glioblastoma. Here we show that STAT3 inhibition leads to the upregulation of the histone H3K27me2/3 demethylase Jmjd3 (KDM6B), which can reverse polycomb complex-mediated repression of tissue specific genes. STAT3 binds to the Jmjd3 promoter, suggesting that Jmjd3 is a direct target of STAT3. Overexpression of Jmjd3 slows glioblastoma stem cell growth and neurosphere formation, whereas knockdown of Jmjd3 rescues the STAT3 inhibitor-induced neurosphere formation defect. Consistent with this observation, STAT3 inhibition leads to histone H3K27 demethylation of neural differentiation genes, such as Myt1, FGF21, and GDF15. These results demonstrate that the regulation of Jmjd3 by STAT3 maintains repression of differentiation specific genes and is therefore important for the maintenance of self-renewal of normal neural and glioblastoma stem cells.
Oxygen Tension Regulates Mitochondrial DNA-encoded Complex I Gene Expression*

Oxygen is a major regulator of nuclear gene expression. However, although mitochondria consume almost all of the O2 available to the cells, little is known about how O2 tension influences the expression of the mitochondrial genome. We show in O2-sensitive excitable rat PC12 cells that, among the mtDNA-encoded genes, hypoxia produced a specific down-regulation of the transcripts encoding mitochondrial complex I NADH dehydrogenase (ND) subunits, particularly ND4 and ND5 mRNAs and a stable mRNA precursor containing the ND5 and cytochrome b genes. This unprecedented effect of hypoxia was fast (developed in <30 min) and fairly reversible and occurred at moderate levels of hypoxia (O2 tensions in the range of 20–70 mm Hg). Hypoxic down-regulation of the mitochondrial complex I genes was paralleled by the reduction of complex I activity and was retarded by iron chelation, suggesting that an iron-dependent post-transcriptional mechanism could regulate mitochondrial mRNA stability. It is known that cell respiration is under tight control by the amount of proteins in mitochondrial complexes of the electron transport chain. Therefore, regulation of the expression of the mitochondrial (mtDNA)-encoded complex I subunits could be part of an adaptive mechanism to adjust respiration rate to the availability of O2 and to induce fast adaptive changes in hypoxic cells.
How Journalists decide which Questions to Ask: Implications for Mobile Knowledge Management

We report on a study of radio journalists conducting meetings, deciding which events to investigate and the extent to which they qualify as news, and, crucially, the practical efforts involved in conducting the interviews and editing the raw recordings into a finished programme. Examining this particular strand of work, it became obvious that in many instances, finding out which questions to ask is much more important than sharing knowledge. Establishing which events may qualify as news is a collective effort, and is currently accomplished in co-located meetings. Since “new news” takes place at an increasing pace, however, there is now very often a need to establish “newsworthiness” in the field, where journalists are intractably mobile and detached from the editorial collective at their radio station. Thus, this paper points to some design implications for mobile knowledge management.
Automatic design of compact multi-band archimedes spiral antenna using capacity coupling

This paper investigates the influence of the capacity coupling on the antenna characteristics. In order to obtain logical results, we adopt the spiral of Archimedes for the scroll configuration and change the mutual and capacity coupling between the meander lines on the layers by changing initial radius r0 and distance d between the layers of the spiral. After basic study of the antenna characteristics when r0 and d are changed using a fixed meander line configuration, we investigate the influence of downsizing the antenna on the mutual and capacity coupling using parallel calculation of the GA (genetic algorithm).
Separable hyperstructure and delayed link binding

As the amount of material on the World Wide Web continues to grow, users are discovering that the Web's embedded, hard-coded, links are difficult to maintain and update. Hyperlinks need a degree of abstraction in the way they are specified together with a sound underlying document structure and the property of separability from the documents they are linking. The case is made by studying the advantages of program/data separation in computer system architectures and also by re-examining some selected hypermedia systems that have already implemented separability. The prospects for introducing more abstract links into future versions of HTML and PDF, via emerging standards such as XPath, XPointer XLink and URN, are briefly discussed.
A high-performance, low-overhead microarchitecture for secure program execution

High performance and low power consumption have traditionally been the primary design goals for computer architects. With computer systems facing a wave of attacks that disrupt their normal execution or leak sensitive data, computer security is no longer an afterthought. Dynamic integrity checking has emerged as a possible solution to protect computer systems by thwarting various attacks. Dynamic integrity checking involves calculation of hashes of the instructions in the code being executed and comparing these hashes against corresponding precomputed hashes at runtime. The processor pipeline is stalled and the instructions are not allowed to commit until the integrity check is complete. Such an approach has severe performance implications as it stalls the pipeline for several cycles. In this paper, we propose a hardware-based dynamic integrity checking approach that does not stall the processor pipeline. We permit the instructions to commit before the integrity check is complete, and allow them to make changes to the register file, but not the data cache. The system is rolled back to a known state if the checker deems the instructions as modified. Our experiments show an average performance overhead of 1.66%, area overhead of 4.25%, and a power overhead of 2.45% over a baseline processor.
"Stray": a new multimedia music composition using the andantephone

The andantephone is an instrument that allows a performed to physically step through a piece of music by walking. Each note or chord of the piece is assigned to one footstep, so expressively varying velocity varies the tempo in turn. A new, more flexible design of andantephone was created for use in a new composition, using an array of tiles sensitive to geophonic seismic waves from footsteps. This user-interface was combined with a real-time frequency shifterbank which shifted the geophonic vibrations of human feet to the frequencies of the musical notes and chords of the composition. Matrix multiplication in the shifterbank allowed chords from various tiles to be expressively layered together depending on the geophonic sounds coming from any number of tiles being stepped on at a time. Moreover, the new shifterbank adjusted its tuning dynamically (according to the composition) as the performer cycled around the track, creating a responsive multitouch landscape that unraveled around the track ahead of and behind the performer. The shifterbank output was also interfaced to a pipe organ, via FLUIDI, using the organ as an additional sounding device. A new andantephone tile configuration led to advantages over previous configurations, including less off-track radial acceleration required to change tempo, and the ability to multiplex between different types of vertex turns, which was found to improve spatial orientation when performing.
Extracting Axially Symmetric Geometry From Limited 3 D Range Data

This paper describes a new, novel low computational-cost approach for recovering geometric structure and pose information of a 3D surface rotationally symmetric about an axis given an unorganized set of 3D range data which covers only a small patch of the surface. Self occluding contours are not seen here. All the parameters necessary to completely define the corresponding surface are estimated. The estimated parameters of the data patch consist of a line describing the axis and a set of parameters which describe the profile curve with respect to the axis. Global algebraic surfaces and local splines consisting of frustrums of cones are used as models for the surface estimation.
Design issues and first experiences with a visual database editor for the extended NF/sup 2/-data model

The authors describe a visual database editor for the extended NF/sup 2/ (eNF/sup 2/)-data model for simple tasks like browsing the database, data entry, and editing. The editor's interface, called a finger, is based on the paradigm of a two-dimensional cursor, and can be used even by casual users. The system, named Escher, serves as a research vehicle for self-referencing methods in the implementation of database systems. One aspect, a fixpoint 'scheme-of-schemes', is discussed in detail, and its visual representation, as produced by the prototype, is shown. Other topics that are treated include the semantics of the cursor movement and new additions to the eNF/sup 2/ data model, such as scripts and links. Preliminary results of the use of Escher are reported. <<ETX>>
“One slash of light, then gone”. Animals as movement

AbstractAnimals are defined by movement. Animals are movement. As Akira Lippit remarks: “The figure of the animal has always been destined to serve as the symbol of movement itself”. Animals never stop moving, never stop moving us, never stop moving across and between the frontiers by which we set them apart. In the invigorated engagement between the social sciences and animal worlds, movement and the sharing of movement offer us the potential for original ways of knowing animals and of understanding our relationship to them. This paper explores that potential and the ontological and ethical consequences it has for living with animals.
Bringing taxonomic structure to large digital libraries

Digital libraries are invaluable repositories of information. However, in many situations, their size makes it difficult to access the desired resource. In this paper, we present an automatic, unsupervised, domain-independent and scalable approach for structuring the resources available in a certain electronic repository for a particular domain. The system automatically detects and extracts the main topics related to the desired domain, offering a taxonomical structure. This result is complemented by the library's search engine, offering an integrated tool for accessing resources as an automatically composed directory service. The system has been tested for several digital libraries and domains of knowledge, providing good quality results in all cases.
A Battery Modeling Method and Its Verification in Discharge Curves of Lead-Acid Batteries

Modeling the external characteristics of the battery precisely is a basic issue for effective battery management in energy storage systems. It is difficult because many inherent factors influence the external characteristics, but only few information, such as terminal voltage, current and surface temperature, can be obtained for modeling. This paper proposes a simple method for modeling the discharge characteristics of the battery. The basic patterns of discharge curves and their relationship with discharge current are analyzed. A mathematic model is built based on the method . The model is verified with experiments on valve-regulated lead-acid (VRLA) batteries.
Rapid hybridization of nucleic acids using isotachophoresis

We use isotachophoresis (ITP) to control and increase the rate of nucleic acid hybridization reactions in free solution. We present a new physical model, validation experiments, and demonstrations of this assay. We studied the coupled physicochemical processes of preconcentration, mixing, and chemical reaction kinetics under ITP. Our experimentally validated model enables a closed form solution for ITP-aided reaction kinetics, and reveals a new characteristic time scale which correctly predicts order 10,000-fold speed-up of chemical reaction rate for order 100 pM reactants, and greater enhancement at lower concentrations. At 500 pM concentration, we measured a reaction time which is 14,000-fold lower than that predicted for standard second-order hybridization. The model and method are generally applicable to acceleration of reactions involving nucleic acids, and may be applicable to a wide range of reactions involving ionic reactants.
A 12b 60MS/s 0.11μm Flash-SAR ADC using a mismatch-free shared sampling network

This work proposes a 12b 60MS/s 0. 11μm CMOS Flash-SAR ADC for wireless communication systems. The proposed Flash-SAR ADC is implemented with a 4b flash ADC and a 9b SAR ADC for high speed operation with low power consumption. Furthermore, the shared single sampling-network minimizes a sampling-time mismatch between the flash ADC and the SAR ADC, which is commonly observed in a Flash-SAR ADC without a T/H circuit. The prototype ADC occupies an active die area of 0.31mm2 and consumes 3.2mW at a 1.2V supply voltage.
Temperature modulation of cerebral depolarization during focal cerebral ischemia in rats: correlation with ischemic injury.

The role of cerebral depolarizations in focal cerebral ischemia is unknown. We therefore measured the direct current (DC) electrical activity in the cortex of Wistar rats subjected to transient occlusion of the middle cerebral artery (MCA). Focal ischemia was induced for 90 min by insertion of an intraluminal filament to occlude the MCA. To modulate cell damage, we subjected the rats to hypothermic (30 degrees C, n = 4), normothermic (37 degrees C, n = 4), and hyperthermic (40 degrees C, n = 6) ischemia. Controlled temperatures were also maintained during 1 h of reperfusion. Continuous cortical DC potential changes were measured using two active Ag-AgCl electrodes placed in the cortical lesion. Animals were killed 1 week after ischemia. The brains were sectioned and stained with hematoxylin and eosin, for evaluation of neuronal damage, and calculation of infarct volume. All animals exhibited an initial depolarization within 30 min of ischemia, followed by a single depolarization event in hypothermic animals, and multiple periodic depolarization events in both normothermic and hyperthermic animals. Hyperthermic animals exhibited significantly more (p < 0.05) DC potential deflections (n = 6.17 +/- 0.67) than normothermic animals (n = 2.75 +/- 0.96). The ischemic infarct volume (% of hemisphere) was significantly different for the various groups; hypothermic animals exhibited no measurable infarct volume, while the ischemic infarct volume was 10.2 +/- 12.3% in normothermic animals and 36.5 +/- 3.4% in hyperthermic animals (p < 0.05). A significant correlation was detected between the volume of infarct and number of depolarization events (r = 0.90, p < 0.001). (ABSTRACT TRUNCATED AT 250 WORDS)
Selectional Restrictions in HPSG

Selectional restrictions are semantic sortal constraints imposed on the participants of linguistic constructions to capture contextually-dependent constraints on interpretation. Despite their limitations, selectional restrictions have proven very useful in natural language applications, where they have been used frequently in word sense disambiguation, syntactic disambiguation, and anaphora resolution. Given their practical value, we explore two methods to incorporate selectional restrictions in the HPSG theory, assuming that the reader is familiar with HPSG. The first method employs HPSG's BACKGROUND feature and a constraint-satisfaction component pipe-lined after the parser. The second method uses subsorts of referential indices, and blocks readings that violate selectional restrictions during parsing. While theoretically less satisfactory, we have found the second method particularly useful in the development of practical systems.