Miracle-dz/UniFAR-FTUs huggingface dataset:
Biased reading frames of pre‐existing DH‐‐JH coding joints and preferential nucleotide insertions at VH‐‐DJH signal joints of excision products of immunoglobulin heavy chain gene rearrangements.

During B cell differentiation immunoglobulin (Ig) DH segments join to JH segments, followed by joining of VH to DJH. Although circular excision products of DH‐‐JH rearrangements have been characterized, excision products of VH to DJH joining have never been isolated. We selectively denatured chromosomal DNA of mouse splenocytes and enriched circular DNA spanning the long distance between VH and DH. Subsequent PCR amplifications allowed the identification of signal joints of VH to DJH. Sequence analysis indicated that preexisting DH‐‐JH coding joints of excision products showed a strong bias for reading frame 1, and the absence of reading frame 2, which would allow the expression of a truncated mu chain called D mu protein. When comparing the joints of the VH‐‐DJH and DH‐‐JH rearrangements we observed N‐nucleotide insertions to be abundant at the VH‐‐DH signal joint, but very sparse at the DH‐‐JH signal joint, while the coding joints of both contained abundant N‐insertions. These differences in N region insertions at the signal joints suggest a differential control of the D‐‐J and V‐‐DJ rearrangements.
Stability of irinotecan-loaded drug eluting beads (DC BeadTM) used for transarterial chemoembolization

Purpose. The aim of this study was to determine the loading efficiency, physicochemical stability, and release of irinotecan-loaded DC BeadsTM (bead size 100—300 μm, 300—500 μm) before and after mixing with nonionic contrast medium (Accupaque® 300, Imeron® 300, Ultravist ® 300) during a prolonged period of time (28 days) when stored at room temperature or refrigerated. Methods. DC Beads TM were loaded with 50 mg irinotecan (Campto®) per milliliter beads in a 2 h loading period. Drug loading efficiency and stability were determined by measuring the irinotecan concentration in the excess solution. A free-flowing in vitro elution method for a period of 2 h and phosphate buffered solution (PBS, pH 7.2) as elution medium were used to analyze the integrity of the irinotecan-loaded. Stability of irinotecan-loaded beads after mixing with an equal volume of three different nonionic contrast agents was determined by measuring irinotecan concentrations in the excess solutions. Vials with loaded beads were stored protected from light at room temperature. Mixtures with contrast media were stored protected from light under refrigeration (2—8°C). Samples were taken periodically over a 4 week period (day 0, 1, 3, 7 and 28). A reversed phase HPLC assay with ultraviolet detection was utilized to analyze the concentration and purity of irinotecan. Results. The loading procedure of DC BeadsTM with irinotecan drug solution resulted in a loading percentage of 96% (bead size 100—300 μm) independent of the storage time. No differences in loading levels and no irinotecan degradation products were observed over the period of 28 days, while the test vials were stored light protected at room temperature. Integrity of loaded irinotecan was also given over that same period of time according to the purity and concentration of irinotecan measured after intentional elution with PBS. Mixing of irinotecan-loaded beads (bead size 100—300 μm, 300—500 μm) with nonionic contrast media decreased the irinotecan loading efficiency by ∼5—10% during a maximum period of 24 h. However, no further elution or degradation was observed during a 4-week period when stored protected from light under refrigeration. Conclusions. Irinotecan-loaded DC BeadsTM are shown to have adequate physicochemical stability over a period of at least 28 days when stored light protected at room temperature. Due to concerns of microbiological overgrowth refrigeration should always be considered. The preparation of admixtures of irinotecan-loaded beads with contrast medium in centralized cytotoxic preparation units is not recommended, because of rapid elution of 5—10% of irinotecan from the loaded beads. Furthermore, physicians see no advantages of admixtures due to the wide variation of mixing ratios of drug-loaded beads with contrast medium. In addition varying volumes of 0.9% sodium chloride solution are to be admixed during the chemoembolization procedure
Enhanced wavelet block tree based image coding algorithm

A novel scheme, “WBTC (wavelet block tree coder) algorithm” that allows a substantial reduction in the storage size of an image is proposed in this work. The coding algorithm is based on the spatial orientation tree (SOT). The major feature of this WBTC algorithm is that it fuses both zero-tree and zero-block algorithm. The key feature of wavelet decomposition is its energy clustering property in space and frequency. When the discrete wavelet transform (DWT) is applied, image is represented by set of wavelet co-efficients. Then the WBTC algorithm is applied and significance is tested at each level. It will partition the image into significant and insignificant blocks. Significant block is quad partitioned into four sub blocks until all the significant co-efficients are found. This procedure is repeated to the next resolution. Performance of the proposed method is compared with the other state-of-art coding algorithms including JPEG2000, SPIHT for many images. Simulation results show that the proposed algorithm has a better coding efficiency over the other coders at very low bit rates.
Extraction of intrinsic response from S-parameters of laser diodes

We describe a new method for extracting the intrinsic response of a laser diode from S-parameters measured using a calibrated vector network analyzer. The experimental results obtained using the new method are compared with those obtained using the optical modulation method and the frequency response subtraction method. Good agreement has been obtained, confirming the new method validity and accuracy. The new method has the advantages of obtaining the intrinsic characteristics of a laser diode with conventional measurements using a network analyzer.
Effect of enamel etching on tensile bond strength of brackets bonded in vivo with a resin-reinforced glass ionomer cement.

OBJECTIVE To evaluate the influence of enamel etching on tensile bond strength of orthodontic brackets bonded with resin-reinforced glass ionomer cement. MATERIALS AND METHODS The sample group consisted of 15 patients who had indications for extraction of four premolars for orthodontic reasons, equally divided into two different groups according to bracket and enamel preparation. Brackets were bonded in vivo, by the same operator, using a split mouth random technique: Group 1 (control), phosphoric acid + Fuji Ortho LC; Group 2, Fuji Ortho LC without acid conditioning. The teeth were extracted after 4 weeks using elevators. An Instron Universal Testing Machine was used to apply a tensile force directly to the enamel-bracket interface at a speed of 0.5 mm/min. The groups were compared using a Mann-Whitney U-test and Weibull analysis. RESULTS Mean results and standard deviations (in MPa) for the groups were: Group 1, 6.26 (3.21), Group 2, 6.52 (2.73). No significant difference was observed in the bond strengths of the two groups evaluated (P = .599). CONCLUSIONS Fuji Ortho LC showed adequate shear bond strength and may be suitable for clinical use.
Target validation and drug discovery using genomic and protein–protein interaction technologies

After the successful completion of the human genome project, mapping of the human proteome has become the next important challenge facing the biotech and pharmaceutical industries. Identification of the ‘right’ target(s) is now a critical part of the process because of the cost of drug discovery. Compounding this situation is the fact that the pharmaceutical industry faces a further challenge of being able to sustain current and historical growth rates. Hence, the discovery of new drug targets is important for developing new drug leads that can become preclinical drug candidates. Proteomics is the next phase of the effort whereby the human genome can be understood. However, mapping the human proteome presents a daunting challenge. Proteomics involves several essential components with the most significant being the discovery and description of all protein–protein interactions. Once this compendium is available, a secondary and equally important initiative will be to decipher proteins that are differentially expressed in any given disease condition. At this point, the critical focus will be to select the most relevant proteins, understand their partner interactions and then further winnow them to the point where they are relevant pharmaceutical target candidates. This paradigm can be compared to finding the relevant ‘needle in the proteome haystack’. This review describes the use of genomic and protein–protein interaction technologies to identify and validate these ‘needles’ as the first step in the drug discovery process.
Genotypic identification of pathogenic Mycobacterium species by using a nonradioactive oligonucleotide probe

Commercial DNA hybridization assays (Syngene, Inc., San Diego, Calif.) utilizing alkaline phosphatase-labeled oligonucleotide probes for the identification of Mycobacterium tuberculosis complex and M. avium complex (MAC) were evaluated with 261 isolates of mycobacteria. On the basis of biochemical criteria, the test for MAC was 98% specific and more sensitive (95 of 99, 95%) than Gen-Probe (88 of 99, 89% sensitivity); the major difference in sensitivity noted between the two systems was related to the hybridization of seven MAC strains to the SNAP X probe. The M. tuberculosis complex probe correctly identified all 62 isolates of M. tuberculosis and all 11 isolates of M. bovis, for a sensitivity of 100%. There were two discrepant reactions with mycobacteria other than M. tuberculosis complex isolates.
Application performance metrics for evaluating delay estimation schemes

Delay estimation schemes have been proposed to estimate the n2 delays between n hosts using only O(n) measurements. Each scheme has been shown accurate when evaluated using an aggregated metric. However, their accuracy is low using metrics that evaluate their quality of estimations as experienced by the application users. Further, their use in several applications produces delay several times higher than optimal. This paper considers five classes of network applications and proposes three delay performance metrics to evaluate IDMaps, GNP, Vivaldi, and IDES when used in these applications. Our metrics measure the user-perceived performance difference of the applications when using estimation instead of direct delay measurement. Our simulations show that while these schemes have shortcomings, the majority of users receive good results for many applications.
Effect of Inflammatory Cytokines on Major Histocompatibility Complex Expression and Differentiation of Human Neural Stem/Progenitor Cells

To develop transplantation of neural stem/progenitor cells (NSPCs) as a successful treatment of neurodegenerative disorders, the possible induction of an inflammatory response following implantation needs to be taken into consideration. Inflammatory cytokines can upregulate major histocompatibility complex (MHC) expression on transplanted cells, thereby rendering them more susceptible to graft rejection. Furthermore, cytokines also have a profound effect on cell differentiation, migration, and proliferation, which can greatly affect the outcome of transplantation. Here we studied the effect of three inflammatory cytokines, interferon‐γ (IFN‐γ), tumor necrosis factor‐α (TNF‐α), and interleukin‐6 (IL‐6), from three different species (human, monkey, rat) on expression of MHC molecules and differentiation of two human NSPC lines derived from striatum and hippocampus. Human and monkey IFN‐γ strongly upregulate MHC expression in both NSPC lines in a dose‐dependent manner, whereas rat IFN‐γ has an effect on MHC expression only in hippocampal cells. Furthermore, TNF‐α, but not IL‐6, upregulates MHC expression in both NSPC lines. Differentiation of NSPCs in the presence of cytokines showed that IFN‐γ increased the neuronal yield threefold in striatal NSPC cultures and increased the number of oligodendrocytes twofold in hippocampal NSPC cultures. Addition of TNF‐α enhanced gliogenesis in both cell lines, whereas IL‐6 stimulated neurogenesis. Human NSPC lines' response to cytokines is therefore species specific and also dependent on the NSPCs' region of origin. The successful translation of different cell lines from animal models to clinical trials could be substantially influenced by the species‐specific regulation of MHC and differentiation as reported here.
Dissociation of synthetic Holliday junctions by E. coli RecG protein.

The RecG protein of Escherichia coli is needed for normal levels of recombination and for repair of DNA damaged by ultraviolet light, mitomycin C and ionizing radiation. The true extent of its involvement in these processes is masked to a large degree by what appears to be a functional overlap with the products of the three ruv genes. RuvA and RuvB act together to promote branch migration of Holliday junctions, while RuvC catalyses the resolution of these recombination intermediates into viable products by endonuclease cleavage. In this paper, we describe the overproduction and purification of RecG and demonstrate that the overlap extends to the biochemistry. We show that the 76 kDa RecG protein is a DNA‐dependent ATPase, like RuvB. Using gel retardation assays we demonstrate that it binds specifically to a synthetic Holliday junction, like RuvA and RuvC. Finally, we show that in the presence of ATP and Mg2+, RecG dissociates these junctions to duplex products, like RuvAB. We suggest that RecG and RuvAB provide alternative activities than can promote branch migration of Holliday junctions in recombination and DNA repair.
Radio frequency interference mitigation in HF passive bistatic radar

HF passive bistatic radar (HFPBR) is a novel and promising technique in development. DRM broadcast transmitters supply good choice for the illuminator of HFPBR, owing to the good signal properties and excellent low-altitude coverage. HFPBR based on DRM broadcast is able to detect targets over the horizon and remotely sense sea states. HFPBR working in crowded short wave band, as the active radar, faces with radio frequency interference (RFI) problem. A temporal adaptive processing method based on the RFI characteristics for HFPBR is introduced in this paper. A closed-form approximate solution of maximum likelihood estimator (MLE) has been derived, to improve the estimate accuracy of RFI parameters. And the performance of the new RFI mitigation algorithm are tested on the real data.
Estimate of Sahelian dust emissions in the intertropical discontinuity region of the West African Monsoon

A three-dimensional mesoscale numerical simulation has been performed to investigate the dust emissions over the Sahel associated with strong near-surface winds in the region of the West African Inter Tropical Discontinuity (ITD) during the summer, when the ITD is located over Niger and Mali around 18°N. The study focuses on the period from 2 to 12 July 2006, in the framework of the African Monsoon Multidisciplinary Analysis (AMMA) Special Observing Period 2a1. The comparison with observations suggests that the model can be used reliably to analyze and quantify the dust emissions associated with the strong near-surface winds blowing over the Sahelian dust sources during the period of interest. The daily mean values of dust load related to the strong winds on both side of the ITD, as estimated from the simulation within the model domain (2°W–16°E, 12–28°N), are in excess of 2 Tg on some of the days of the 2–12 July 2006 period. In the present case, the dust load associated with the strong winds south of the ITD accounts for between one third and two thirds of the total load mobilized in the ITD region over the entire domain on a given day. It is simulated to range between 0.5 and 0.8 Tg on average. This study suggests that emissions driven by strong surface winds occurring on both sides of the ITD while lying across the Sahel may contribute significantly to the total dust load over West and North Africa observed annually.
An Algorithm for Finding the Causal Distributed Breakpoint

Acausal distributed breakpointis one of the fundamental mechanisms for debugging distributed programs. It is initiated by a sequential breakpoint in one process of a distributed computation, and restores each process to theearlieststate that reflects all events that happened causally before the sequential breakpoint. This paper presents an algorithm for finding the causal distributed breakpoint when a sequential breakpoint occurs. To find the causal distributed breakpoint efficiently, some information about dependency of events is piggybacked in every message and is logged at each process. The algorithm requiresO(1) information in each message and finds the causal distributed breakpoint inO(nlogn+m) time, wherendenotes the number of processes andmdenotes the number of distinct pairs of processes directly communicating with each other.
E-business in the developing world: an empirical study of payment methods and their implications

The recent trend of outsourcing manufacturing and services from the developed economies is creating buoyant economies in the developing world. With advances in technological infrastructure, these new markets are being transformed by e-business. In this paper, we discuss issues regarding methods of payment for internet purchases in China, India and Pakistan. The relationship between factors that may influence the establishment and growth of e-business within these economies are investigated empirically. A logit model of payment method preference is subsequently developed from these analyses. Finally, a general discussion regarding obstacles, limitations and ways forward for e-business in these economies is provided.
Identification of active-site residues in protease 3C of hepatitis A virus by site-directed mutagenesis

Picornavirus 3C proteases (3Cpro) are cysteine proteases related by amino acid sequence to trypsin-like serine proteases. Comparisons of 3Cpro of hepatitis A virus (HAV) to those of other picornaviruses have resulted in prediction of active-site residues: histidine at position 44 (H44), aspartic acid (D98), and cysteine (C172). To test whether these residues are key members of a putative catalytic triad, oligonucleotide-directed mutagenesis was targeted to 3Cpro in the context of natural polypeptide precursor P3. Autocatalytic processing of the polyprotein containing wild-type or variant 3Cpro was tested by in vivo expression of vaccinia virus-HAV chimeras in an animal cell-T7 hybrid system and by in vitro translation of corresponding RNAs. Comparison with proteins present in HAV-infected cells showed that both expression systems mimicked authentic polyprotein processing. Individual substitutions of H44 by tyrosine and of C172 by glycine or serine resulted in complete loss of the virus-specific proteolytic cascade. In contrast, a P3 polyprotein in which D98 was substituted by asparagine underwent only slightly delayed processing, while an additional substitution of valine (V47) by glycine within putative protein 3A caused a more pronounced loss of processing. Therefore, apparently H44 and C172 are active-site constituents whereas D98 is not. The results, furthermore, suggest that substitution of amino acid residues distant from polyprotein cleavage sites may reduce proteolytic activity, presumably by altering substrate conformation.
Architecture‐driven assistance for fault‐localization tasks

Finding software faults is a problematic activity in many systems. Existing approaches usually work close to the system implementation and require developers to perform different code analyses. Although these approaches are effective, the amount of information to be managed by developers is often overwhelming. This problem calls for complementary approaches able to work at higher levels of abstraction than code, helping developers to keep intellectual control over the system when analyzing faults. In this context, we present an expert‐system approach, called FLABot, which assists developers in fault‐localization tasks by reasoning about faults using software architecture models. We have evaluated a prototype of FLABot in two medium‐size case studies, involving novice and non‐novice developers. We compared time consumed, code browsed and faults found by these developers, with and without the support of FLABot, observing interesting effort reductions when applying FLABot. The results and lessons learned have shown that our approach is practical and reduces the efforts for finding individual faults.
Analysis of the Coupling Effect in Different Meander-Type Winding Planar Transformers

In this paper, planar printed-circuit board (PCB) transformers with different winding arrangements are presented. Three different arrangements of the primary and the secondary meander-type windings are designed and fabricated. The electrical parameters of the transformers for all three designs are analyzed and compared. A significant increase of inductance of the primary and the secondary winding is achieved with an appropriate meander-type winding arrangement. In the frequency range of interest, the inductance is approximately 145 nH for the first design, whereas the inductance is approximately 1250 nH for the second and the third design. The coupling coefficient is 0.14 for the first design, whereas it is around 0.9 for the second and the third design. The transformer of the proposed design is to be used in low-power DC/DC converters; therefore, the core with high permeability Ferroxcube 3C90 was chosen. In addition, the transformers of the same winding arrangements were tested with Ferroxcube 3F3 core.
Percutaneous coronary intervention of or through saphenous vein grafts or internal mammary arteries: The impact of stents, adjunctive pharmacology, and multicomponent distal protection

We hypothesized that the use of stents and aggressive adjunctive pharmacotherapies has been associated with lower rates of complicating myocardial infarction (MI) and improved long‐term outcomes compared to either previous balloon‐only percutaneous coronary intervention (PCI) or atheroablative intervention for lesions of or through saphenous vein grafts (SVGs) and/or internal mammary arteries (IMAs). PCI of SVG has been complicated by relatively high rates of procedural MI and less favorable long‐term outcomes than native vessel PCI, stimulating the development and application of an array of technologies. This study was based on retrospective review of stent‐era (1999–2004) 5‐year experience of a single center with 95 SVG procedures in 85 patients and 20 IMA procedures in 20 patients. These cases were compared with the previously published experience of one of the operators during the balloon‐only period and literature review of the application of multiple technologies to SVG intervention, as well as consideration of the reoperation alternative. There was one in‐hospital death each in the SVG cohort (1%) and in the IMA cohort (5%). There were SIX procedural MIs (6%), defined by total CK > normal, and 19 procedural MIs (20%) based on troponin‐I > 1.0. Follow‐up has been from 4 months to 5 years (average, 2.5 years), with 91% survival and one late CABG in the IMA group. SVG PCI with stents and adjunctive pharmacotherapies is associated with relatively low rates of procedural MI and favorable long‐term outcomes. Published 2006 Wiley‐Liss, Inc.