Miracle-dz/UniFAR-FTUs huggingface dataset:
Cervical Spine Outcomes Questionnaire: Its Development and Psychometric Properties

Study Design. A cross-sectional study was conducted to analyze a convenience sample of patients seeking treatment for cervical spine conditions. Objective. To develop and evaluate the psychometric properties of a comprehensive, disease-specific questionnaire for characterizing complaints of neck pain and evaluating the outcomes of treatments for these complaints. Summary of Background Data. There currently are a number of generic and disease-specific instruments for assessing complaints of neck pain. None comprehensively cover the wide range of factors considered essential in evaluating treatment outcomes. Methods. The authors developed a comprehensive, disease-specific questionnaire for characterizing complaints of neck pain and evaluating the outcomes of treatments for these complaints. In this study, 216 patients who underwent surgery for cervical spine disorders completed the Cervical Spine Outcomes Questionnaire before treatment, then at 3 and 6 months after treatment. The data were used to evaluate the reliability, validity, and responsiveness of the questionnaire. Results. The authors have shown that the Cervical Spine Outcomes Questionnaire has high test–retest reliability, good construct validity, and responsiveness to change after treatment. Conclusions. The Cervical Spine Outcomes Questionnaire is a comprehensive, disease-specific instrument for assessing complaints of neck pain and evaluating the outcomes of treatments for these complaints. It provides information on demographics, pain severity, functional disability, psychological distress, physical symptoms, health care utilization, and satisfaction. It appears to be acceptable to patients, easy to administer, highly reliable, valid, and responsive. It should be considered for use in monitoring patients with cervical spine conditions and in studies of cervical spine disorders and their treatments.
“Using’ what we got”: Calculating X‐ray Spectra for Non‐Equilibrium Plasmas

It is desirable to calculate the X‐ray emission spectrum from a (region of a) plasma that is not in ionization equilibrium, e.g., with application to supernova remnants, SNRs. Such a plasma will generally have ionization fractions that are not directly related to the local electron temperature and, in the case of SNR ejecta, may contain little or no H and He. This work describes the use of a currently available database, ATOMDB, and software, ISIS, to generate spectra for a non‐equilibrium ionization, NEI, plasma which is specified by explicit densities and ionization fractions and an independent electron temperature. An example spectrum is shown and discussed. The approach here does have some deficiencies currently: not all relevant inner‐shell lines are included, there are no Cr lines, and continua spectra are not given on an ion‐by‐ion basis. Finally, in the low density, NEI case, it may be useful to consider the emission components that arise from each “quiescent” ion.
Efficacy of a five-drug combination including ritonavir, saquinavir and efavirenz in patients who failed on a conventional triple-drug regimen: phenotypic resistance to protease inhibitors predicts outcome of therapy.

OBJECTIVE to assess the safety and efficacy of a combination of ritonavir, efavirenz and two recycled nucleosides in patients who failed on a conventional triple-drug regimen including indinavir or ritonavir. METHODS An open label study of ritonavir (100 mg twice daily), saquinavir (1000 mg twice daily), efavirenz (600 mg per day) and nucleoside analogues in 32 saquinavir- and efavirenz-naive protease inhibitor-experienced patients. Patients were included on the basis of plasma levels of HIV RNA above 5000 copies/ml while on conventional antiretroviral therapy. Phenotypic resistance and genotypic resistance mutations to saquinavir were assessed at baseline. Peak and trough plasma levels of saquinavir were monitored throughout the study. RESULTS Median CD4 cell counts and median plasma HIV RNA at baseline were 258 x 10(6)/l and 4.31 log10 copies/ml, respectively. The plasma viral load decreased by a median of 1.20 log10 copies/ml and the CD4 cell count increased by a median 60 x 10(6) cells/l at week 24 of therapy. Seventy-one per cent of the patients achieved a plasma viral load < 500 copies/ml and 45% achieved a viral load < 50 copies/ml. Patients exhibiting phenotypic resistance to saquinavir at baseline experienced a median decrease in HIV RNA of 0.91 log10 copies/ml at week 24 of therapy, as compared with a decrease of 1.52 log10 copies/ml in those exhibiting sensitive viral strains (P = 0.03). Genotypic resistance to saquinavir was not predictive of virologic failure. CONCLUSION Our results indicate that the combination of ritonavir, saquinavir and efavirenz is safe and effective at 24 weeks in over two-thirds of patients who previously failed on highly active antiretroviral therapy, and that the determination of phenotypic resistance may be of greater value than the detection of resistance mutations to predict the outcome of salvage therapy in this setting.
SeaWASP: A small waterplane area twin hull autonomous platform for shallow water mapping

Students with Santa Clara University (SCU) and the Monterey Bay Aquarium Research Institute (MBARI) are developing an innovative platform for shallow water bathymetry. Bathymetry data is used to analyze the geography, ecosystem, and health of marine habitats. However, current methods for shallow water measurements typically involve large, manned vessels. These vessels may pose a danger to themselves and the environment in shallow, semi-navigable waters. Small vessels, however, are prone to disturbance by the waves, tides, and currents of shallow water. The SCU / MBARI autonomous surface vessel (ASV) is designed to operate safely, stably in waters > 1 m and without significant manned support. Final deployment will be at NOAA's Kasitsna Bay Laboratory in Alaska. The ASV utilizes several key design components to provide stability, shallow draft, and long-duration unmanned operations. Bathymetry is measured with a multibeam sonar in concert with DVL and GPS sensors. Pitch, roll, and heave are minimized by a Small Waterplane Area Twin Hull (SWATH) design. The SWATH has a submerged hull, small water-plane area, and high mass to damping ratio, making it less prone to disturbance and ideal for accurate data collection. Precision sensing and actuation is controlled by onboard autonomous algorithms. Autonomous navigation increases the quality of the data collection and reduces the necessity for continuous manning. The vessel has been operated successfully in several open water test environments, including Elkhorn Slough, CA, Steven's Creek, CA, and Lake Tahoe, NV. It is currently is in the final stages of integration and test for its first major science mission at Orcas Island, San Juan Islands, WA, in August, 2008. The Orcas Island deployment will feature design upgrades implemented in Summer, 2008, including additional batteries for all-day power (minimum eight hours), active ballast, real-time data monitoring, updated autonomous control electronics and software, and data editing using in-house bathymetry mapping software, MB-System. This paper will present the results of the Orcas Island mission and evaluate possible design changes for Alaska. Also, we will include a discussion of our shallow water bathymetry design considerations and a technical overview of the subsystems and previous test results. The ASV has been developed in partnership with Santa Clara University, the Monterey Bay Aquarium Research Institute, the University of Alaska Fairbanks, and NOAA's West Coat and Polar Regions Undersea Research Center.
Monitoring Preparation of Derivative Protein Crystals via Raman Microscopy

Below to crystallographic applications, protein crystals are of great interest in other numerous fields of biology and biotechnology. Cataract, or the loss of transparency of the eye lens, is related to the alteration of physical, chemical, and structural properties of proteins of the crystallin family, that may lead to crystallization under some physiological conditions (Tardieu, 1998). Other pathological states are known to be a consequence of the in vivo formation of crystals, made of either proteins or other macromolecular assemblies. Examples are viral proteins stored in plant cells, viral particles in animal cells, hemoglobin C and S causing anemia, or ribosomal particles accumulating in the brain of patients suffering from presenile dementia (McPherson, 1999). Of course, crystals of biological macromolecules that are prepared in vitro have important applications: they are tools to obtain atomic models of the molecules and to design specific ligands and new drug formulations. Medicinal formulations composed of either insulin (Richards et al., 1999) or α-interferon crystals (Reichert et al., 1996) are already applied in treatments to ensure the continuous release of protein in blood. Crystallographic analysis of highly ordered crystals with intense X-ray sources provides accurate three dimensional structures (Ducruix & Giege, 1999). The success of this technique strictly depends on obtaining diffraction-quality crystals. The process of crystallization remains a hit-and-miss affair, typically involving screening hundreds of conditions. The crystallization of biological macromolecules shares many common properties with those of small solute molecules (e.g. growth by 2D nucleation or by screw dislocation mechanisms), but their crystals exhibit several peculiarities: most of them have a high solvent content (e.g. 30-80 vol%), few intermolecular contacts, and a high density of defects (Malkin et al., 1996). Briefly, protein crystallization requires the formation of a supersaturated protein-precipitant solution. The transition from a stable solution to a supersaturated one can be achieved by increasing the concentration of precipitant and/or that of protein (Vergara et al., 2003). The most frequently used crystallization method is the vapor diffusion technique. A drop containing protein, buffer, salt and precipitant is equilibrated against a reservoir (buffer, salt and precipitant). The difference in concentration between the drop (lower) and the reservoir (higher) drives the system toward equilibrium by diffusion through the vapor phase. The drop can either be placed on the underside of the cover slide (hanging drop) or placed on a
Comparison of pharmacokinetic variables for creatinine and iohexol in dogs with various degrees of renal function.

OBJECTIVE To compare pharmacokinetics and clearances of creatinine and iohexol as estimates of glomerular filtration rate (GFR) in dogs with various degrees of renal function. ANIMALS 50 Great Anglo-Francais Tricolor Hounds with various degrees of renal function. PROCEDURES Boluses of iohexol (40 mg/kg) and creatinine (647 mg/kg) were injected IV. Blood samples were collected before administration and 5 and 10 minutes and 1, 2, 4, 6, and 8 hours after administration. Plasma creatinine and iohexol concentrations were assayed via an enzymatic method and high-performance liquid chromatography, respectively. A noncompartmental approach was used for pharmacokinetic analysis. Pharmacokinetic variables were compared via a Bland-Altman plot and an ANOVA. RESULTS Compared with results for creatinine, iohexol had a significantly higher mean ± SD plasma clearance (3.4 ± 0.8 mL/min/kg vs 3.0 ± 0.7 mL/min/kg) and a significantly lower mean volume of distribution at steady state (250 ± 37 mL/kg vs 539 ± 73 mL/kg), mean residence time (80 ± 31 minutes vs 195 ± 73 minutes), and mean elimination half-life (74 ± 20 minutes vs 173 ± 53 minutes). Despite discrepancies between clearances, especially for high values, the difference was < 0.6 mL/min/kg for 34 (68%) dogs. Three dogs with a low GFR (< 2 mL/min/kg) were classified similarly by both methods. CONCLUSIONS AND CLINICAL RELEVANCE Plasma iohexol and creatinine clearances can be used interchangeably for screening patients suspected of having chronic kidney disease (ie, low GFR), but large differences may exist for dogs with a GFR within or above the reference range.
Androgenic regulation of hedgehog signaling pathway components in prostate cancer cells

Hedgehog signaling is thought to play a role in several human cancers including prostate cancer. Although prostate cancer cells express many of the gene products involved in hedgehog signaling, these cells are refractory to the canonical signaling effects of exogenous hedgehog ligands or to activated Smoothened, the hedgehog-regulated mediator of Gli transcriptional activation. Here, we show that the expression of hedgehog ligands and some hedgehog target genes are regulated by androgen in the human prostate cancer cell line, LNCaP and its more metastatic variants (C4-2 and C4-2B). Androgen (R1881) strongly suppressed the expression of hedgehog ligands in these cells and their prolonged maintenance in androgen-deficient medium upregulated Sonic and Indian hedgehog mRNA and protein levels by up to 30,000-fold. Hedgehogs were released into the conditioned medium of androgen-deprived LNCaP cells and this medium was able to increase hedgehog target gene expression in hedgehog-responsive mouse fibroblasts (MC3T3-E1). Moreover, this activity was accompanied by increased expression of Gli target genes, Patched 1 and Gli2, in LNCaP that could be suppressed by cyclopamine, indicating that chronic androgen-deprivation also re-awakens the autocrine responsiveness of the cancer cells to hedgehog. In contrast to the suppressive effects of R1881 on hedgehog ligand and Gli2 expression, we found that Gli1 expression in LNCaP cells was induced by R1881. Given the ability of androgen to modulate the expression and release of hedgehog ligands and the activity of the autocrine hedgehog signaling pathway in these prostate cancer cells, our results imply that chronic androgen deprivation therapy (ADT) for prostate cancer might create a hedgehog signaling environment in the region of the tumor that could ultimately impact on the long term effectiveness of this treatment. This consideration supports the idea of clinically testing hedgehog-blocking drugs in conjunction with ADT in patients with advanced prostate cancer.
Research on the relationship between knowledge grey generation and innovation performance in knowledge-based enterprises

The knowledge grey generation process in knowledge-based enterprises consists of the merging, recombination, splitting and deletion of knowledge units, which is the smallest behavior unit of the transformation from internal knowledge to value. This paper establishes a knowledge grey generation model of the knowledge-based enterprises to study the relationship between knowledge grey generation and innovation performance. Through simulation analysis, it concludes that the knowledge grey generation strength can influence the innovation performance differently in the enterprises of different innovation modes. Specifically, in the initial stage of knowledge generation, the innovation performance increases with the knowledge grey generation strength; with time evolution, the innovation performance will be down after it gets the maximum; the rules of the relationship between knowledge grey generation strength and innovation performance are different under different innovation modes.
Sustained expression of coagulation factor IX by modified cord blood‐derived mesenchymal stromal cells

Hemophilia B patients are subject to frequent and spontaneous bleeding caused by a deficiency of clotting factor IX (FIX). Mesenchymal stromal cells (MSCs) have been used in cellular therapies as a result of their immunomodulatory properties, the ability to home to sites of injury and their amenability to various ex vivo modifications, including lentiviral‐mediated gene transfer.
Approaches to samples selection for machine learning based classification of textual data

The paper focuses on retrieval of relevant documents written in a natural language based on availability of several candidate examples which are used as the basis for the automatic selection of only items that are similar to these predefined patterns. Presented approach should face problems related to processing user created content in natural language that include a poor control over the topic and the structure of the content and often also huge computational complexity. Three methods of selecting the best samples from a large set of candidate samples are presented - random selection, manual selection and a new approach called automatic biased sample selection, and measures based on Euclidean distance and cosine similarity are used for classification. The experiments are carried out with real world data consisting of customer reviews downloaded from amazon.com, converted to different representations based on bag-of-words procedure. The experiments and the results of the presented approach provided satisfactory values and can lead to an alternative approach to manual selection and evaluation of textual samples.
A client-entropy measure for On-line Signatures

In this article, we propose an original way to characterize information content in online signatures through a client-entropy measure based on local density estimation by a hidden Markov model. We show that this measure can be used to categorize signatures in visually coherent classes that can be related to complexity and variability criteria. Besides, the generated categories are coherent across four different databases: BIOMET, MCYT-100, BioSecure data subsets DS2 and DS3. This measure allows a comparison of databases in terms of clientspsila signatures according to their information content.
The RING Finger Ubiquitin E3 Ligase SDIR1 Targets SDIR1-INTERACTING PROTEIN1 for Degradation to Modulate the Salt Stress Response and ABA Signaling in Arabidopsis

An endoplasmic reticulum-bound ubiquitin E3 ligase targets its chloroplast/nucleus-bound substrate for degradation to promote abscisic acid signaling and the salt stress response. The plant hormone abscisic acid (ABA) regulates many aspects of plant development and the stress response. The intracellular E3 ligase SDIR1 (SALT- AND DROUGHT-INDUCED REALLY INTERESTING NEW GENE FINGER1) plays a key role in ABA signaling, regulating ABA-related seed germination and the stress response. In this study, we found that SDIR1 is localized on the endoplasmic reticulum membrane in Arabidopsis thaliana. Using cell biology, molecular biology, and biochemistry approaches, we demonstrated that SDIR1 interacts with and ubiquitinates its substrate, SDIRIP1 (SDIR1-INTERACTING PROTEIN1), to modulate SDIRIP1 stability through the 26S proteasome pathway. SDIRIP1 acts genetically downstream of SDIR1 in ABA and salt stress signaling. In detail, SDIRIP1 selectively regulates the expression of the downstream basic region/leucine zipper motif transcription factor gene ABA-INSENSITIVE5, rather than ABA-RESPONSIVE ELEMENTS BINDING FACTOR3 (ABF3) or ABF4, to regulate ABA-mediated seed germination and the plant salt response. Overall, the SDIR1/SDIRIP1 complex plays a vital role in ABA signaling through the ubiquitination pathway.
BAYESIAN ESTIMATION OF PARAMETERS IN HODGKIN-HUXLEY ́ S MODEL OF BIOMEDICAL ELECTRIC SIGNALS

Hodgkin and Huxley, in their classical paper of 1952 proposed that the action potential in excitable cells, such as axons or Purkinje fibers, can be modeled in terms of an electric circuit with capacitance and ionic electrical currents. Sodium and Potassium ions are the most influential in the action potential and are distinguished in terms of their own proper currents, in comparison to other ions. In this paper, we apply the Markov Chain Monte Carlo (MCMC) method for the estimation of parameters appearing in Hodgkin-Huxley ́s model, by using simulated measurements of the action potential. The MCMC method is implemented in the form of the Metropolis-Hastings' algorithm. An analysis of the sensitivity coefficients is used for the selection of the prior distributions for the parameters. The parameters are successfully estimated with Gaussian priors, even with associated large variances and large measurement errors.
Application of biologically-oriented dentin bonding principles to the use of endodontic irrigants.

PURPOSE To compare the removal of smear layer and the structure of the hybrid layer formed after the use of EDTA or MTAD solutions when used as a final flush. METHODS Single-rooted extracted premolars (n=18) were collected and treated for root canal therapy using NaOCl irrigation followed by a final rinse of 17% EDTA, Biopure MTAD, or saline (negative control). The roots were obturated with gutta-percha and a hydrophilic HEMA-containing root canal sealer. The TEM specimens were impregnated with 50% silver nitrate to visualize sealing imperfections and nanoleakage. The structure of the coronal, middle and apical parts of root canal walls was examined using transmission electron microscopy. RESULTS After NaOCl irrigation, a final rinse with BioPure MTAD or 17% EDTA completely removed the 2 microm-thick smear layer on mechanically instrumented root canal walls. The BioPure MTAD hybrid layer was thicker than the 17% EDTA hybrid layer. Both the BioPure MTAD and EDTA caused a collapse of the dentin matrix structure which impeded sealer infiltration and the formation of high quality hybrid layer bonding. The hybrid layers created in smear layer-covered dentin exhibited less potential for nanoleakage than the MTAD or EDTA hybrid layers.
Introduction to Editorial Board Members: Professor David A. Tirrell

In this second issue of Bioengineering and Translational Medicine, we are pleased to introduce our Editorial Board Member, Prof. David A. Tirrell. Prof. Tirrell is the Ross McCollum-William H. Corcoran Professor of Chemistry and Chemical Engineering and Director of the Beckman Institute at California Institute of Technology. He earned his BS degree in Chemistry at Massachusetts Institute of Technology and his PhD in Polymer Science and Engineering at University of Massachusetts Amherst. Professor Tirrell’s research has made a deep impact on multiple fields including synthetic polymers, membranes, and artificial proteins. His pioneering research in artificial proteins has been particularly inspiring. Artificial proteins are hybrids between synthetic polymers and natural proteins. They may contain amino acids beyond the canonical 20 in the genetic code, and/or amino acid sequences not found in naturally occurring proteins, which endow these proteins with functions well beyond their natural counterparts. Since artificial proteins are produced from artificial genes by cellular transcription and translation processes, they have defined length, sequence, and structure that enable functions such as binding and catalysis, which are not possible by inherently heterogeneous synthetic polymers. Professor Tirrell has
Polarization reconfigurable loop antenna for satellite communications

This paper presents a polarization reconfigurable printed loop antenna which could alter its polarization states electronically to right-hand circular polarization (RHCP), left-hand circular polarization (LHCP) or linear polarization (LP). By inserting four PIN diodes into the symmetric gaps of a dual-loop planar antenna, the proposed antenna can switch its polarization status by controlling the on-off state of PIN diodes electronically. Meanwhile, a coplanar stripline (CPS) has been employed as an impedance transformer for this antenna. It is shown that the antenna can achieve a 5.4% 3-dB AR bandwidth with a wider impedance bandwidth of 12.5% for both RHCP and LHCP and a 7.1% impedance bandwidth for LP. The proposed antenna has a uni-directional radiation pattern with a peak gain of 9.8 dBi under all polarization status. The presented antenna can achieve polarization reconfigurability and a high gain, while having a low profile and low cost. It is promising for applications in satellite communications and terrestrial wireless communication systems.