Miracle-dz/UniFAR-FTUs huggingface dataset:
Complexity of FGF receptors: genetic basis for structural diversity and functional specificity

Since 1989, the receptors for fibroblast growth factors (FGFs) were cloned and characterized as a subgroup of the family of receptor tyrosine kinases. Four FGF receptor genes were identified, all of which encode membrane‐bound glycoproteins containing three immunoglobulin (Ig) ‐like domains at the extracellular region, where only two of these domains are involved in ligand binding. Three unique features characterize the FGF receptors: 1) overlapping recognition and redundant specificity, where one receptor may bind with a similar affinity several of the seven known FGFs and one FGF may bind similarly to several distinct receptors. 2) The binding of FGFs to their receptors is dependent on the interaction of FGF with cell surface heparan sulfate proteoglycans. 3) A multitude of isoforms of cell‐bound or secreted receptors are produced by the same gene. The gene structure of these receptors revealed two major mechanisms that are responsible for the formation of the diverse forms: alternative mRNA splicing, resulting in deletions or alternate exons usage, and internal polyadenylation, resulting in truncated products. These are reminiscent of mechanisms that also operate in the immunoglobulin family to generate diversity and to produce either secreted or cell‐bound molecules. Tissue‐specific alternative splicing in FGF receptors allows for the generation of two distinct receptors from a single gene because alternative exons determine the sequence of the COOH‐terminal half of the third Ig‐like domain involved in ligand binding. This represents a novel genetic mechanism to generate receptor diversity and specificity and to increase receptor repertoire. — Givol, D. ; Yayon, A. Complexity of FGF receptors: genetic basis for structural diversity and functional specificity. FASEB J. 6: 3362‐3369; 1992.
Effect of Ultrasound-Enhanced Transdermal Drug Delivery Efficiency of Nanoparticles and Brucine

Brucine is the active component in traditional Chinese medicine “Ma-Qian-Zi” (Strychnos nux-vomica Linn), with capabilities of analgesic, anti-inflammatory, anti-tumor and so on. It is crucial how to break through the impact of cuticle skin which reduces the penetration of drugs to improve drug transmission rate. The aim of this study is to improve the local drug concentration by using ultrasound. We used fresh porcine skin to study the effects of ultrasound on the transdermal absorption of brucine under the influence of various acoustic parameters, including frequency, amplitude and irradiation time. The transdermal conditions of yellow-green fluorescent nanoparticles and brucine in skin samples were observed by laser confocal microscopy and ultraviolet spectrophotometry. The results show that under ultrasonic conditions, the permeability of the skin to the fluorescent label and brucine (e.g., the depth and concentration of penetration) is increased compared to its passive diffusion permeability. The best ultrasound penetration can make the penetration depth of more than 110 microns, fluorescent nanoparticles and brucine concentration increased to 2-3 times. This work will provide supportive data on how the brucine is better used for transdermal drug delivery (TDD).
Term Structure of Commodities Futures . Forecasting and Pricing

The development of risk management methodologies for non-gaussian markets relies often on the assumption that the underlying market factors have a gaussian distribution. While advances have been made in the modeling of more general marginal distributions of the risk factors, the modeling of non-gaussian dependence structures is much less advanced. For commodities markets that often exhibit sudden changes from backwardation into contango (such as energy, agricultural products and metals), correlations or linear transformations of them fail to account for realistic transformations of forward curve convexity. This paper develops a model that overcomes this difficulty for scenario generation purposes. It also provides the “risk neutral” processes needed for derivatives pricing, answering two leading problems of the financial world (forecasting and pricing), and presents it in the context of other developments for commodity futures modeling.
Negative microbiological results are not mandatory in deep sternal wound infections before wound closure.

OBJECTIVES To define the outcome of treatment for deep sternal wound infections (DSWIs) using direct wound closure (DC) or vacuum-assisted therapy (VAT) based on negative vs. positive microbiological results. METHODS Between 1999 and 2008, 7746 patients underwent median sternotomy for cardiac surgery at our institution. Patients were screened for DSWI and out of the cohort 159 were identified (2%). These patients were treated, either using DC or VAT with delayed wound closure. Outcomes were retrospectively analysed to determine the effect of negative cultures at the time of closure. RESULTS The indication for sternotomy was CABG 51%, isolated valve 18%, CABG/valve 18% and other related cardiovascular procedures 14%. Sixty-five percent of the wound infections was diagnosed during rehabilitation period. One hundred and five (66%) patients were treated with VAT vs. 54 (34%) patients with direct closure. Coagulase negative staphylococci were found in 48% of bacterial cultures. In 75% of the patients, the microbiological results were positive at time of wound closure (69.2% VAT vs. 87.0% direct closure, P = 0.014). Out of 159 patients, 5.0% were with positive microbiological results at the time of closure readmitted vs. 5.1% with negative microbiological results (P = 1.0). Patients with VAT stayed significantly longer in the hospital (mean 21 ± 16 vs. 13 ± 12, P = 0.002). CONCLUSIONS Negative microbiological results are not mandatory before wound closure, as the rate of readmissions for recurrence of infection showed no difference between groups. Our results also suggest that shortening of VAT despite positive microbiological results may be feasible.
Self-Referencing and Persuasion: Narrative Transportation versus Analytical Elaboration

This article contrasts narrative self-referencing with analytical self-referencing. I propose that narrative self-referencing persuades through transportation, where people become absorbed in a story-in this case, in their storylike thoughts (Green and Brock 2000 ). When ad viewers are transported by these narrative thoughts, persuasion is not negatively affected by weak ad arguments. Conversely, analytical self-referencing persuades via more traditional processing models, wherein cognitive elaboration is enhanced by relating incoming information to one's self or personal experiences, which results in a differential persuasive effect of strong versus weak arguments. I also propose that ad skepticism moderates the effect of narrative transportation. My assertions are tested in two experiments in the context of mental simulation as a form of narrative self-referencing. (c) 2007 by JOURNAL OF CONSUMER RESEARCH, Inc.
Efficiency effects of agricultural economics research in the United States

Allocations of research funds across programs are often made for efficiency reasons. Social science research is shown to have small, lagged but significant effects on U.S. agricultural efficiency when public agricultural R&D and extension are simultaneously taken into account. Farm management and marketing research variables are used to explain variations in estimates of allocative and technical efficiency using a Bayesian approach that incorporates stylized facts concerning lagged research impacts in a way that is less restrictive than popular polynomial distributed lags. Results are reported in terms of means and standard deviations of estimated probability distributions of parameters and long-run total multipliers. Extension is estimated to have a greater impact on both allocative and technical efficiency than either R&D or social science research.
Distribution of the catabolic transposon Tn5271 in a groundwater bioremediation system

The distribution of Tn5271-related DNA sequences in samples of groundwater and a groundwater bioremediation system at the Hyde Park (Niagara Falls, N.Y.) chemical landfill site was investigated. PCR amplification of target sequences within the cha genes of Tn5271 revealed similar sequences in the groundwater community and in samples from the sequencing batch reactors treating that groundwater. Cell dilution combined with PCR amplification indicated that cha sequences were carried in about 1 of 10 culturable bacteria from the treatment system. Characterization of isolates involved in chlorobenzoate and toluene biodegradation in the treatment system indicated that two phenotypic clusters, Alcaligenes faecalis type 2 and CDC group IVC-2, contained all of the Tn5271 probe-positive isolates from the community. These two groups differed phenotypically from recipient groups isolated following horizontal transfer of pBRC60 (Tn5271) in pristine freshwater microcosms. A genetic rearrangement in Tn5271 attributable to the intramolecular transposition of the flanking element IS1071R was detected in an isolate from the treatment system. Comparison of the structure of the intramolecular transposition derivative from groundwater isolate OCC13(pBRC13) with a laboratory-derived intramolecular transposition derivative of pBRC60 revealed similarities. The rearrangement was shown to increase the stability of the plasmid under starvation conditions.
The Effect of Intra-articular Corticosteroids on Articular Cartilage

Background: Intra-articular (IA) corticosteroid therapy has been used for the treatment of inflammation and pain in the knee since the 1950s. Purpose: To review the current literature on the effects of IA corticosteroids on articular cartilage. Study Design: Systematic review. Methods: A MEDLINE and SCOPUS database search was performed, and studies were selected for basic science and clinical trial research on corticosteroids with direct outcome measures of cartilage health. Preliminary searches yielded 1929 articles, and final analysis includes 40 studies. Results: Methylprednisolone, dexamethasone, hydrocortisone, betamethasone, prednisolone, and triamcinolone were reported to display dose-dependent deleterious effects on cartilage morphology, histology, and viability in both in vitro and in vivo models. The beneficial animal in vivo effects of methylprednisolone, hydrocortisone, and triamcinolone occurred at low doses (usually <2-3 mg/dose or 8-12 mg/cumulative total dose in vivo), at which increased cell growth and recovery from damage was observed; the single human clinical trial indicated a beneficial effect of triamcinolone. However, at higher doses (>3 mg/dose or 18-24 mg/cumulative total dose in vivo), corticosteroids were associated with significant gross cartilage damage and chondrocyte toxicity. Dose and time dependency of corticosteroid chondrotoxicity was supported in the in vitro results, however, without clear dose thresholds. Conclusion: Corticosteroids have a time- and dose-dependent effect on articular cartilage, with beneficial effects occurring at low doses and durations and detrimental effects at high doses and durations. Clinically, beneficial effects are supported for IA administration, but the lowest efficacious dose should be used.
Proteasome Inhibitors Block Development ofPlasmodium spp

ABSTRACT Proteasomes degrade most of the proteins inside eukaryotic cells, including transcription factors and regulators of cell cycle progression. Here we show that nanomolar concentrations of lactacystin, a specific irreversible inhibitor of the 20S proteasome, inhibit development of the exoerythrocytic and erythrocytic stages of the malaria parasite. Although lactacystin-treated Plasmodium berghei sporozoites are still invasive, their development into exoerythrocytic forms (EEF) is inhibited in vitro and in vivo. Erythrocytic schizogony of P. falciparum in vitro is also profoundly inhibited when drug treatment of the synchronized parasites is prior, but not subsequent, to the initiation of DNA synthesis, suggesting that the inhibitory effect of lactacystin is cell cycle specific. Lactacystin reduces P. berghei parasitemia in rats, but the therapeutic index is very low. Along with other studies showing that lactacystin inhibits stage-specific transformation inTrypanosoma and Entamoeba spp. , these findings highlight the potential of proteasome inhibitors as drugs for the treatment of diseases caused by protozoan parasites.
An empirical study of constraint usage in graphical applications

One-way constraints have been widely incorporated in research toolkits for constructing graphical applications. However, although a number of studies have examined the performance of these toolkits’ constraint satisfaction algorithms, there have not been any empirical studies that have examined how programmers use constraints in actual applications. This paper reports the results of a study intended to address these matters. Seven graphical applications were chosen for their diversity and profiling information was gathered about their use of constraints, The data reveal that constraint networks tend to be modular, that is, divided into a number c~fsmall, independent sets of constraints rather than one mono] ithic set of constraints. This finding suggests that constraint satisfaction algorithms should be able to resatisfy constraints rapidly after a change to one or more variables. It also suggests that debugging constraints should not be unduly burdensome on a programmer since the number of constraints that must be examined to find the source of an error is not terriblly large. Overall, the results of this study should provide a repository of data that will be useful in directing future research on optimizing constraint solvers and developing effective debugging techniques.
Light and electron microscopic immunocytochemical localization of AMPA‐selective glutamate receptors in the rat spinal cord

α‐Amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionate (AMPA)‐type glutamate receptors are probably the most widespread excitatory neurotransmitter receptors of the central nervous system, and they play a role in most normal and pathological neural activities. However, previous detailed studies of AMPA subunit distribution have been limited mainly to the brain. Thus, a comprehensive study of AMPA receptor subunit distribution was carried out on sections of rat spinal cord and dorsal root ganglia, which were immunolabeled with antibodies made against peptides corresponding to C‐terminal portions of the AMPA receptor subunits: GluR1, GluR2/3, and GluR4. In the spinal cord. Labeling was most prominent in the superficial dorsal horn, motoneurons, and nuclei containing preganglionic autonomic neurons. Immunostaining also was observed in neurons in other regions including those known to contain Renshaw cells and Ia Inhibitory cells. Although overall immunostaining was lighter with antibody to GluR1 than with GluR2/3 and 4, there were neurons were neurons that preferentially stained with antibody to GluR1. These “GluR1 intense” neurons were usually fusiform and most concentrated in lamina X. In dorsal root ganglia, immunostaining of ganglion cell bodies was moderate to dense with antibody to GluR2/3 and light to moderate with antibody to GluR4. Possible neuroglia in the spinal cord (mainly GluR2/3 and 4) and satellite cells in dorsal root ganglia (GliR4) were immunostained. Electron microscopic studies of the the superficial dorsal horn and lateral motor column showed staining that was restricted mainly to postsynaptic densities and associated dendritic and cell body cytoplasm. In dorsal horn, colocalization of dense‐cored vesicles with clear, round synaptic vesicles was observed in unstained presynaptic terminals apposed to stained postsynaptic densities. Subsynaptic dense bodies (Taxi‐bodies) were associated with some stained postsynaptic densities in the superficial dorsal horn and lateral motor column. Based on several morphological features including vesicle structure and presence of Taxi‐bodies, it is likely that at least some of the postsynaptic staining seen in this study is apposed to glutamatergic input from primary sensory afferent terminals. © 1994 Wiley‐Liss, Inc.
Multifunctional PEG Retinylamine Conjugate Provides Prolonged Protection against Retinal Degeneration in Mice

A polyethylene glycol (PEG) retinylamine (Ret-NH2) conjugate PEG-GFL-NH-Ret with a glycine-phenylalanine-leucine (GFL) spacer was synthesized for controlled oral delivery of Ret-NH2 to treat retinal degenerative diseases, including Stargardt disease (STGD) and age-related macular degeneration (AMD). The peptide spacer was introduced for sustained release of the drug by digestive enzymes in the gastrointestinal tract. The pharmacokinetics experiments showed that the PEG conjugate could control the sustained drug release after oral administration and had much lower nonspecific liver drug accumulation than the free drug in wild-type female C57BL mice. In the mean time, the conjugate maintained the same concentration of Ret-NH2 in the eye as the free drug. Also, PEG-GFL-NH-Ret at a Ret-NH2 equivalent dose of 25 mg/kg produced complete protection of Abca4–/–Rdh8–/– mouse retinas against light-induced retinal degeneration for 3 days after oral administration, as revealed by OCT retina imaging, whereas free Ret-NH2 did not provide any protection under identical conditions. The polymer conjugate PEG-GFL-NH-Ret has great potential for controlled delivery of Ret-NH2 to the eye for effective protection against retinal degenerative diseases.
Cervical thymic hyperplasia after chemotherapy in an adult patient with Hodgkin lymphoma: a potential cause of false‐positivity on [18F]FDG PET/CT scanning

A 30-year-old woman was referred for a positron emission tomography/computed tomography (PET/CT) scan with [F]fluorodeoxyglucose ([F]FDG) for staging of Hodgkin lymphoma (HL), nodular sclerosis type, diagnosed by biopsy of a bulky mediastinal mass. The scan demonstrated tracer uptake in the cervical lymph nodes bilaterally, in the bulky mediastinal mass and in the lungs, spleen and some lumbar and sacral vertebral bodies (top left). A PET/CT scan performed 1 month after completion of treatment (doxorubicin, bleomycin, vinblastine, dacarbazine, six cycles) showed complete metabolic response (centre of top left image). This finding was confirmed by another PET/CT performed 3 months later. Seven months after the end of chemotherapy, a follow-up PET/CT showed an intense tracer uptake [standardized uptake value (SUV)max = 4AE1 g/ml] in the left supraclavicular region (black arrow, right of top left image), suspicious for lymph node recurrence of HL. A contrast enhanced CT performed 3 d after the PET/CT showed a 20 · 14 mm oval nodule located medially to the jugular vein, suspicious for malignant adenopathy (lower left). A fused PET/ CT axial image showed increased [F]FDG uptake in the solid component of the nodule (right of lower left image). The lesion was resected. Histopathological examination (right) showed well-represented thymic compartments, including cortical (white arrow) and medullary areas (white arrowhead). In addition, a well-formed Hassal’s corpuscle was recognizable (black arrow) (Haematoxylin and Eosin, 200·). Thymic hyperplasia after chemotherapy is a common phenomenon in children and can occasionally be observed in young adults. This phenomenon has seldom been described in older adults. A normal variant in which the thymus extends superiorly to the left brachiocephalic vein and anteriorly to the brachiocephalic artery or left common carotid artery can occur. This can be visualized on CT as a soft tissue nodule that can mimic superior mediastinal adenopathy. In paediatric patients, [F]FDG uptake in a superior mediastinal nodule can be correctly attributed to ectopic thymus whether the intensity of [F]FDG SUVmax or the morphological characteristics are similar to the thymus. In the present case, the lack of significant thymic activity, the absence of thymic enlargement in the anterior mediastinum, the cervical involvement at first diagnosis, and the CT appearance of the soft tissue nodule led to the erroneous suspicion of recurrence of lymphoma. This report shows that increased [F]FDG uptake in hyperplastic ectopic thymic tissue following chemotherapy can also occur in adult patients. This rare normal variant should be kept in mind in PET/CT studies in patients with HL.
Effect of wall shear rate on biofilm deposition and grazing in drinking water flow chambers

The effect of four‐wall shear rates (34.9, 74.8, 142.5, and 194.5 s−1) on bacterial deposition on glass slides in drinking water flow chambers was studied. Biofilm image acquisition was performed over a 50‐day period. Bacterial accumulation and surface coverage curves were obtained. Microscopic observations allowed us to obtain information about the dynamics and spatial distribution of the biofilm. During the first stage of biofilm formation (210–518 h), bacterial accumulation was a function of the wall shear rate: the higher the wall shear rate, the faster the bacterial deposition (1.1 and 1.9 × 104 bacterial cells · cm−2 for wall shear rates of 34.9 and 142.5 s−1, respectively). A new similarity relationship characteristic of a non‐dimensional time and function of the wall shear rate was proposed to describe initial bacterial deposition. After 50 days of exposure to drinking water, surface coverage was more or less identical under the entire wall shear rates (7.44 ± 0.9%), suggesting that biofilm bacterial density cannot be controlled using hydrodynamics. However, the spatial distribution of the biofilm was clearly different. Under low wall shear rate, aggregates were composed of bacterial cells able to “vibrate” independently on the surface, whereas, under a high wall shear rate, aggregates were more cohesive. Therefore, susceptibility to the hydraulic discontinuities occurring in drinking water system may not be similar. In all the flow chambers, significant decreases in bacterial biomass (up to 77%) were associated with the presence of amoebae. This grazing preferentially targeted small, isolated cells. Biotechnol. Bioeng. 2007; 97: 1550–1561. © 2007 Wiley Periodicals, Inc.
Satisfiability models and algorithms for circuit delay computation

The existence of false paths represents a significant and computationally complex problem in the estimation of the true delay of combinational and sequential circuits. In this article we conduct a comprehensive study of modeling circuit delay computation, accounting for false paths, as a sequence of instances of Boolean satisfiability. Several path sensitization models and delay models are studied. In addition we evaluate some of the most competitive Boolean satisfiability algorithms seeking to identify which are best suited for solving circuit delay computation problems. Finally, realistic delay modeling (taking into account extracted interconnect delays and fanout data) is considered in order to experimentally evaluate the complexity of solving real-world instances.