Miracle-dz/UniFAR-FTUs huggingface dataset:
In vitro splicing of mutually exclusive exons from the chicken beta‐tropomyosin gene: role of the branch point location and very long pyrimidine stretch.

The chicken beta‐tropomyosin gene contains 11 exons, two of which are spliced into mRNA only in skeletal muscle. One pair of alternative exons, 6A and 6B, is found in the middle of the gene; they are spliced in a mutually exclusive manner. The non‐muscle splice 6A‐7 is by far the predominant in vitro reaction in a HeLa cell nuclear extract. A minor product is the 6A‐6B splice, which is excluded in all tissues. This minor product results from the use of a branch point located 105 nt upstream of the 3′ end of the intron separating exons 6A and 6B. The region between the branch point sequence and the final AG contains a stretch of approximately 80 pyrimidines. We have examined the role of the distance of the branchpoint to the 3′ splice site and of the sequences between these two elements. Our results suggest that at least two cis‐acting elements contribute to the mutual exclusivity of exons 6A and 6B. The intron between exons 6A and 6B is intrinsically poorly ‘spliceable’ both because the branch point is too far upstream of the 3′ end of the intron to give efficient splicing and because of the particular sequence lying between this branch point and the 3′ splice site.
Characterization of genomic DNA encoding cecropins from an Aedes albopictus mosquito cell line

We used cDNA probes from Aedes albopictus mosquito cecropins AalCecA, B, and C to obtain genomic DNA copies and flanking DNA. Two gene copies (AalCecA1 and A2, AalCecB1 and B2, AalCecC1 and C2) encoding each of the three mature cecropin peptides were recovered. All these genes had a similar organization, into two exons interrupted by a single short intron. AalCecA1 and AalCecA2 encode mature protein products that differ by one amino acid residue, while AalCecB1 and AalCecB2, AalCecC1 and AalCecC2 encode identical mature cecropin peptides, respectively. The AalCecB and C gene pairs each share a common intergenic region of approximately 1 kb, with the two coding regions transcribed in opposite directions. With the exception of small insertions/deletions, the intergenic spacer region was highly conserved between the B1/C1 and B2/C2 clones. In transfected cells, 0.8 kb of upstream sequence was sufficient for inducible expression of AalCecA1. Within this region, a 28 bp sequence at positions –192 to –165 upstream of the transcription initiation site was found to contain a potential regulatory element. In electrophoretic mobility shift assays, synthetic double‐stranded DNA containing this 28 bp sequence retarded protein in cytoplasmic and nuclear extracts from C7‐10 cells.
Dual-band reconfigurable bandstop filter with independently controlled stopbands and constant absolute bandwidths

This paper presents a novel reconfigurable dual-band bandstop filter with independently controlled stopbands and constant absolute bandwidths (ABWs). The fundamental structure is based on λ/4 varactor-loaded resonators, and the key to constant ABW is choosing proper coupling regions between resonators. Theoretical analysis and calculation are carried out to determine physical parameters of the coupling regions. For demonstration, a second-order dual-band bandstop filter is implemented with 23.6% fractional tuning range of the first stopband from 1.27 to 1.57 GHz and 18.1% of the second stopband from 1.98 to 2.34 GHz, and 3-dB ABWs are 60 ± 3 MHz and 103 ± 5 MHz, respectively.
COMPARISON OF IMMEDIATE VERSUS EARLY LOADED DENTAL IMPLANTS IN THE POSTERIOR MANDIBLE USING RESONANCE FREQUENCY ANALYSIS

INTRODUCTION: The clinical measurement of implant stability and osseointegration is important to be able to assess success in implant dentistry. It is now possible to measure implant stability at any time during the course of implant treatment and loading. OBJECTIVE: This study was designed to compare the implant stability of both the immediately and the early loaded dental implants in the posterior mandible by resonance frequency analysis using Osstell ISQ. MATERIALS AND METHODS: Fourteen patients were included in this study (n=14). They were divided in two groups; group I (n=7) and group II (n=7). Group I: Seven patients having missing mandibular molars received an implant in the posterior mandible followed by immediate loading of provisional restoration (immediate loading). Group II: Seven patients having missing mandibular molars received an implant in the posterior mandible and the provisional restoration delivered one month post-insertion (early loading). All patients received dentium superline implant system with an SLA (sandblasted and acid etched) surface. Implant stability quotient (ISQ) was measured using resonance frequency analysis by the OsstellTM device (Osstell Mentor) wireless device. The implant stability was measured immediately post-operative and on intervals of 1, 3 and 6 months. RESULTS: The mean implant stability values in immediate and early loading immediately post-operatively was 69.0±10.71, 61.86±14.22 respectively. There was an increase after 3rd month to be 71.29±2.14, 75.86±3.18 respectively. The implant stability continued to increase after 6th month to be 71.29±4.61, 77.71±1.60 respectively. The increase in implant stability after 3rd and 6th month was statistically significant. CONCLUSION: The mean implant stability quotient (ISQ) increased throughout the follow-up period. KEY WORDS: implant stability, immediate loading, resonance frequency analysis.
Nematocysts of the Invasive Hydroid Cordylophora caspia (Cnidaria: Hydrozoa)

Although there is significant genetic diversity among populations of the hydroid Cordylophora caspia, the species has not been split into multiple species or subspecies, in part because its members also show great physiological and morphological plasticity. This plasticity makes new taxonomic units hard to define or identify and obscures the connection between historically used names and the genetically defined clades. We explore variation in nematocysts, a character system not previously assessed in Cordylophora but which has demonstrated phylogenetic signal in other cnidarian taxa. We measured more than 5000 capsules from 112 individuals belonging to 14 populations, including representatives of the major genetic lineages. We found no correlation between the size range of capsules and either clade or salinity. Thus, for C. caspia, nematocysts are neither phenotypically plastic with respect to salinity nor taxonomically informative. Nematocyst size and density in particular tissues may be correlated to other environmental factors (such as prey type, size, and abundance in the location of each population) and may aid in distinguishing more distantly related species.
Profile: Ewan Birney. Genomics' big talker.

A self-taught programmer turned bioinformatician at the European Bioinformatics Institute (EBI), Ewan Birney has used his gift of gab to pull together 442 researchers to characterize not just the genes but also all the functional elements in the human genome. The Encyclopedia of DNA Elements (ENCODE) project this week published 30 scientific papers that begin to fill in the details of DNA9s role in making life possible (see p. 1159). Birney was in charge of data analysis, and, along with his right-hand man, EBI9s Ian Dunham, he coordinated the setting of quality standards, the development of consistent protocols, and the planning of the publications as well as developing new ways to look at data.
HIV-Specific Antibodies But Not T-Cell Responses Are Associated With Protection in Seronegative Partners of HIV-1-Infected Individuals in Cambodia

Summary: To study biological factors related to protection against HIV-1 infection in Cambodia, we recruited 48 partners of HIV-1-infected patients who remained uninfected (exposed uninfected individuals, EUs) despite unprotected sexual intercourse for more than 1 year and 49 unexposed controls (UCs). HIV-1-specific antibodies (IgA anti-gp41 and IgG anti-CD4-gp120 complex), T-cell responses, and cellular factors that may be involved in protection (peripheral blood mononuclear cell [PBMC] resistance to HIV-1 infection and &bgr;-chemokine production) were evaluated. Anti-HIV-1 antibodies were higher in EUs than those in UCs (P = 0.01 and P = 0.04 for anti-gp41 and anti-CD4-gp120, respectively). We observed a decreased susceptibility to a primary Cambodian isolate, HIV-1KH019, in EU PBMCs as compared with UC PBMCs (P = 0.03). A weak T-cell response to one pool of HIV-1 Gag peptides was found by ELISpot in 1 of 19 EUs. Whereas T-cell specific immunity was not associated to protection, our results suggest that HIV-specific humoral immunity and reduced cell susceptibility to infection may contribute to protection against HIV-1 infection in Cambodian EUs.
Nucleus-specific alteration of raphe neurons in human neurodegenerative disorders

Neurodegenerative diseases share symptoms suggested to be related to the serotonergic system. To evaluate the involvement of serotonergic raphe nuclei, we compared the percentage of neurons synthesizing serotonin in the nucleus centralis superior (NCS), raphe obscurus and pallidus (NROP) in Alzheimer's disease (AD), progressive supranuclear palsy (PSP), Parkinson's disease (PD), multiple system atrophy (MSA), and control brains. We used immunohistochemistry for tryptophan hydroxylase (TpOH), phosphorylated tau, and &agr;-synuclein. We observed a significant decrease in the NCS in the NROP in AD, but a significant increase in PSP and MSA. Cytoskeletal pathology was present in the NCS and NROP to a variable degree. We conclude that there is disease- and nucleus-specific alteration of serotonin synthesis in the raphe.
A sensing system for simultaneous measurement of temperature and transversal loading based on a fiber-ring microwave photonic filter

In this paper, a fiber-optic sensing system for simultaneous measurement of temperature and transversal loading based on a fiber-ring microwave photonic filter (MPF) has been proposed and experimentally demonstrated. The temperature variation will induce the central frequency shift of the MPF's passband, while the micro-bend loss induced by transversal loading will cause the change of extinction ratio of the MPF. Hence, by tracking the central frequency and extinction ratio of the passbands, temperature and transversal loading can be monitored respectively. The proposed sensing system enjoys high sensitivity, remoting sensing, good multiplexing capacity, thus shows a good prospect in practical applications.
FIONA1 Is Essential for Regulating Period Length in the Arabidopsis Circadian Clock[W]

In plants, the circadian clock controls daily physiological cycles as well as daylength-dependent developmental processes such as photoperiodic flowering and seedling growth. Here, we report that FIONA1 (FIO1) is a genetic regulator of period length in the Arabidopsis thaliana circadian clock. FIO1 was identified by screening for a mutation in daylength-dependent flowering. The mutation designated fio1-1 also affects daylength-dependent seedling growth. fio1-1 causes lengthening of the free-running circadian period of leaf movement and the transcription of various genes, including the central oscillators CIRCADIAN CLOCK-ASSOCIATED1, LATE ELONGATED HYPOCOTYL, TIMING OF CAB EXPRESSION1, and LUX ARRHYTHMO. However, period lengthening is not dependent upon environmental light or temperature conditions, which suggests that FIO1 is not a simple input component of the circadian system. Interestingly, fio1-1 exerts a clear effect on the period length of circadian rhythm but has little effect on its amplitude and robustness. FIO1 encodes a novel nuclear protein that is highly conserved throughout the kingdoms. We propose that FIO1 regulates period length in the Arabidopsis circadian clock in a close association with the central oscillator and that the circadian period can be controlled separately from amplitude and robustness.
Regulation of pancreatic insulin and glucagon secretion.

Homeostatic regulation of metabolic fuels involves the generally opposing actions of insulin and glucagon. As most agents simultaneously affect secretion of both hormones, this review attempts, when possible, to discuss regulation of insulin and glucagon secretion as related events. The effects of stimulators and inhibitors of insulin and glucagon secretion have been systematically investigated in vivo and in vitro (116,208,244,287, 322). The underlying molecular mechanisms are usually studied by measurement of islet metabolites, cyclic nucleotides, ions, and macromolecules, but holistic interpreta­ tion of these data is complicated by: (a) difficulties in measuring changes with time; (b) the functional significance of cellular compartments; and (c) the limited number of parameters that can be measured simultaneously. These difficulties are com­ pounded for glucagon because normal islets contain 15-30% A cells. Although islets comparatively rich in A cells derived from animals treated with alloxan or streptozotocin have been used to study A-cell secretory biology (31, 186,257), these cells may not be normal, as they have been chronically subjected to a diabetic environment. This problem may be minimized by maintaining such islets in tissue culture-a procedure that retains the high A-cell population and its response to
Efficient, image-based appearance acquisition of real-world objects

Two ingredients are necessary to synthesize realistic images: an accurate rendering algorithm and, equally important, high-quality models in terms of geometry and reflection properties. In this dissertation we focus on capturing the appearance of real world objects. The acquired model must represent both the geometry and the reflection properties of the object in order to create new views of the object with novel illumination. Starting from scanned 3D geometry, we measure the reflection properties (BRDF) of the object from images taken under known viewing and lighting conditions. The BRDF measurement require only a small number of input images and is made even more efficient by a view planning algorithm. In particular, we propose algorithms for efficient image-to-geometry registration, and an image-based measurement technique to reconstruct spatially varying materials from a sparse set of images using a point light source. Moreover, we present a view planning algorithm that calculates camera and light source positions for optimal quality and efficiency of the measurement process. Relightable models of real-world objects are requested in various fields such as movie production, e-commerce, digital libraries, and virtual heritage.
Underwater depth imaging using time-correlated single photon counting

We investigate the potential of a depth imaging system for underwater environments. This system is based on the timeof- flight approach and the time correlated single-photon counting (TCSPC) technique. We report laboratory-based measurements and explore the potential of achieving sub-centimeter xyz resolution at 10’s meters stand-off distances. Initial laboratory-based experiments demonstrate depth imaging performed over distances of up to 1.8 meters and under a variety of scattering conditions. The system comprised a monostatic transceiver unit, a fiber-coupled supercontinuum laser with a wavelength tunable acousto-optic filter, and a fiber-coupled individual silicon single-photon avalanche diode (SPAD). The scanning in xy was performed using a pair of galvonometer mirrors directing both illumination and scattered returns via a coaxial optical configuration. Target objects were placed in a 110 liter capacity tank and depth images were acquired through approximately 1.7 meters of water containing different concentrations of scattering agent. Depth images were acquired in clear and highly scattering water using per-pixel acquisition times in the range 0.5-100 ms at average optical powers in the range 0.8 nW to 120 μW. Based on the laboratory measurements, estimations of potential performance, including maximum range possible, were performed with a model based on the LIDAR equation. These predictions will be presented for different levels of scattering agent concentration, optical powers, wavelengths and comparisons made with naturally occurring environments. The experimental and theoretical results indicate that the TCSPC technique has potential for highresolution underwater depth profile measurements.
Study on Gas Discharge at Atmospheric Air by Numerical Method

The progress and characteristics of gas discharge is studied in this paper by numerical simulation. A program based on the FE-FCT method in its full two-dimension form is developed and employed for the solution of transport equations of charged species under the effect of space-charge electric field. Results of two-dimensional simulation of cylindrically symmetric streamers in air between Point-plane electrodes are presented. The formation and propagation of streamer is numerically observed. The electric field distribution, streamer speed, radius of streamer channel predicted by the model is in good agreement with experimental measurement. The influence of applied voltage on the streamer characteristic is also investigated.
The winding method and model of a superconducting bending dipole for hadrontherapy

The cancer therapy (hadrontherapy) with accelerated particle beams is an innovative method that allows an accurate and effective treatment of several kinds of tumors minimizing the irradiation of the surrounding tissues and avoiding intercepting vital organs. The deep tumors are usually treated with proton or ion beams by using a rotating gantry that allows the 360/spl deg/ irradiation of the patient. For the carbon ion hadrontherapy, being the energy in the order of 400 MeV, huge gantry structures are required if resistive magnets are used. An alternative solution was studied, involving the use of a cryogenic free superconducting magnet. The magnet consists of ten 90/spl deg/ bent superconducting dipoles wound with an aluminum stabilized Cu/NbTi conductor and mechanically supported by an aluminum alloy structure. In order to validate the feasibility of such a magnet, an accurate study of the winding technique was carried out, together with a winding test of a coil prototype.
Human Muscle Power Output During Upper‐and Lower‐Body Exercises

The purpose of this study was to evaluate the use of traditional resistance training equipment in the measurement of muscular power. This was accomplished by measuring the velocity of movement through a measured distance during maximal effort lifts using a Smith rack. The reliability of the method was established using 10 male volunteers who performed both bench press and squat exercises in a Smith rack. Maximal power output was determined at 30, 40, 50, 60, 70, 80, and 90% of the subject's 1 repetition maximum (1RM). Test-retest power values were not statistically different. Another 15 male volunteers who had previous muscle biopsy data from the vastus lateralis muscle performed the same maximal power output evaluation. There were no significant relationships between peak power outputs and fiber-type expressions when linear regressions were performed. The power curve produced by graphing power output vs. the percentage of 1RM indicates that peak power output occurs between 50 and 70% of 1RM for the squat and between 40 and 60% of 1RM for the bench press. These data indicate that this method of evaluation of muscle power is reliable, although it is not predictive of muscle fiber-type percentages.
Introducing innovations into open source projects

This thesis presents a qualitative study using Grounded Theory Methodology on the question of how to change development processes in Open Source projects. The mailing list communication of thirteen medium-sized Open Source projects over the year 2007 was analyzed to answer this question. It resulted in eight main concepts revolving around the introduction of innovation, i.e.\ new processes, services, and tools, into the projects including topics such as the migration to new systems, the question on where to host services, how radical Open Source projects can change their ways, and how compliance to processes and conventions is enforced. These are complemented with (1) the result of five case studies in which innovation introductions were conducted with Open Source projects, and with (2) a theoretical comparison of the results of this thesis to four theories and scientific perspectives from the organizational and social sciences such as Path Dependence, the Garbage Can model, Social-Network analysis, and Actor-Network theory. The results show that innovation introduction is a multifaceted phenomenon, of which this thesis discusses the most salient conceptual aspects. The thesis concludes with practical advice for innovators and specialized hints for the most popular innovations. %%%%Diese Dissertation widmet sich der Fragestellung, wie Technologien, Werkzeuge und Prozesse der Softwaretechnik in Open-Source-Projekte eingefuhrt werden konnen. Zur Beantwortung dieser Frage werden 13 mittelgrose Open-Source-Projekte mit Hilfe der Grounded Theory Methodology untersucht und die gewonnenen Erkenntnisse in acht Kernkategorien konzeptualisiert. Betrachtet werden unter anderem die Bereitstellung von Infrastrukturressourcen, Entscheidungsmechanismen, Adaptertechnologien, soziale und technische Masnahmen zur Einhaltung von Normen und Standards, die teilweise Einfuhrung von Technologien in fragmentierten Innovationslandschaften und die Rolle von Zeit innerhalb von Innovationseinfuhrungen. Diese Theoriebausteine werden einerseits durch funf Fallstudien in den Bezug zur praktischen Durchfuhrung von Innovationseinfuhrung gestellt und andererseits durch einen Vergleich mit existierenden Theorien aus der Organisations- und Sozialwissenschaft wie z.B. Actor-Network Theory, Social Network Analysis, oder das Garbage Can Modell auf einer theoretischen Ebene betrachtet. Die Arbeit beschreibt Innovationseinfuhrung als breitgefachert zu verstehendes Phanomen, welches sich nicht auf einzelne, konzeptuelle Zusammenhange reduzieren lasst. Die Arbeit schliest mit praktischen Handlungsanleitungen mit besonderem Fokus auf haufig auftretende Innovationsklassen, wie Versionskontrollsysteme, Softwarelizenzen und Defektverwaltungssysteme.
Multistage Model for Distribution Expansion Planning With Distributed Generation—Part I: Problem Formulation

This paper presents a model for use in the problem of multistage planning of energy distribution systems including distributed generation. The expansion model allows alternatives to be considered for increasing the capacity of existing substations, for installing new ones, for using distributed generation, and for the possible change to feeders in terms of addition and removing feeders sections; combining, subdividing, and load transfer between feeders; and replacement of conductors. The objective function to be minimized is the present value of total installation costs (feeders and substations), of operating and maintaining the network, and of distributed generation. The model takes operational constraints on equipment capacities and voltage limits together into account with logical constraints, aimed at reducing the search space. This paper presents: (1) an extension to the linear disjunctive formulation to represent the inclusion, exclusion, and replacement of branches and (2) a generalization of constraints related to the creation of new paths which can be applied in more complex topologies. The resulting mixed integer linear model allows the optimal solution to be found using mathematical programming methods, such as the branch-and-bound algorithm. The validity and efficiency of the model are demonstrated in Part II of this paper.