cssi/SciSciGPT-SciSciNet huggingface dataset:
Differential inflammatory response dynamics in normal lung following stereotactic body radiation therapy with protons versus photons

Abstract Background and purpose To compare time-dependent changes in lung parenchyma of early-stage non-small cell lung carcinoma (NSCLC) patients after stereotactic body radiation therapy with protons (SBPT) or photons (SBRT). Materials and method We retrospectively identified NSCLC patients treated with SBPT and matched each one with a SBRT patient by patient, tumor, and treatment characteristics. Lung parenchyma on serial post-treatment chest computer tomography (CT) scans was deformably registered with the treatment plan to analyze lung density changes as function of dose, quantified by Houndsfield Unit (HU)/Gy. A thoracic radiologist also evaluated the CTs using an established grading system. Results We matched 23 SBPT/SBRT pairs, including 5 patients treated with both modalities (internally matched cohort). Normal lung response following SBPT significantly increased in the early time period (CTs acquired 6 HU/Gy) patients and in the internally matched cohort. However, there was no significant difference in the maximum observed response in the entire cohort over all time periods, median 3.4 [IQR, 1.0–5.4] HU/Gy (SBPT) versus 2.5 [1.6–5.2] HU/Gy (SBRT). Qualitative radiological evaluation was highly correlated with the quantitative analysis (p Conclusion While there was no significant difference in maximum response after SBPT versus SBRT, dose-defined lung inflammation occurred earlier after proton irradiation. Further investigation is warranted into the mechanisms of inflammation and therapeutic consequences after proton versus photon irradiation.
Evaluation of a Genetic Risk Score for Diagnosis of Psoriatic Arthritis

Background:Diagnosis of psoriatic arthritis (PsA) can be challenging, resulting in delays that contribute to irreversible joint damage, reduced quality of life, and increased mortality.Objective:Us...
Taking Temperature with Leaves: A Semester-Long Structured- Inquiry Research Investigation for Undergraduate Plant Biology

Inquiry- and course-based research pedagogies have demonstrated effectiveness for preparing undergraduate biology students with authentic scientific skills and competencies, yet many students lack the experience to engage successfully in open-ended research activities without sufficient scaffolding and structure. Further, curricula for student-centered laboratory activities are lacking for several biological disciplines, including plant biology and botany. In this article, I describe a semester-long structured-inquiry research curriculum developed for a plant biology course taught to second-year biology students that integrates key elements of inquiry and discovery while providing a structured approach to gaining research skills. In the research project, students collect leaves from woody dicot plants across a range of environments that are characterized by different mean annual temperatures, and investigate the relationship between various leaf characteristics and temperature. Curricular materials are provided to teach skills in scientific paper reading, field data collection, data processing including microscopy and image analysis, quantitative data analysis in R, biological inference, and scientific writing. This comprehensive, ready-to-implement curriculum is suitable for plant biology, botany, and plant ecology courses and is particularly valuable for students with no prior research experience.
Treatment of 21 pediatric patients with pulmonary artery sling combined with tracheal stenosis

Objective Total 21 pulmonary artery sling(PA sling) combined with tracheal stenosis children who received treatment in our hospital were reviewed.The feasibility of treatment strategy including left pulmonary artery(LPA) re-implantation without tracheoplasty was discussed in this study. Methods From April 2009 to November 2015, a total of 21 pediatric patients received surgical treatment due to PA sling with tracheal stenosis.Six patients received LPA re-implantation and trachea intervention simultaneously.The other 15 patients received LPA re-implantation alone to relieve the trachea compression without tracheoplasty.The postoperative strategy including early extubation and CPAP ventilation was employed in PICU. Results A total of 21 PA sling with tracheal stenosis children who underwent surgical treatment in our hospital were recruited.There were 9 females and 12 males.Ages of these children were from 1 months to 10 years old, and body weights were from 2.9 kg to 25.0 kg.Five patients needed mechanical ventilation for severe respiratory symptoms preoperatively.Six patients received LPA re-implantation and tracheal intervention simultaneously.Among them, 3 patients received slide tracheoplasty, and one was discharged after recovery.The remaining 3 patients received tracheal stent implantation, but finally died.The survival rate was 16.7% in these patients.Fifteen patients received LPA re-implantation alone, and slide tracheoplasty was performed in 2 patients for extubation failure who finally died of air leakage.The survival rate of 15 patients who received LPA re-implantation alone was 86.7%. Conclusion The strategy in LPA re-implantation alone to relieve the trachea compression without tracheoplasty and early extubation and CPAP ventilation postoperative may be an ideal treatment for the pediatric patients with PLA sling combined with tracheal stenosis. Key words: Pulmonary artery sling; Tracheal stenosis; Left pulmonary artery re-implantation,
Pelvic bone tumor resection: post-operative imaging

The anatomic extent of a pelvic bone tumor and the need for reconstruction dictate the type of pelvic resection (limb salvage pelvic resection or amputation). If a pelvic bone tumor resection involves two or more critical anatomic structures (the sciatic nerve, femoral neurovascular bundle or the hip joint), then reasonable functional recovery after limb salvage is less likely and amputation should be considered. Both limb salvage and amputation approaches to the pelvis are technically arduous surgeries with significant associated morbidity and complications. As such, imaging plays an important role in the post-operative management of patients who have undergone pelvic bone tumor resection. In this article, we will review optimal imaging techniques as well as the expected post-operative appearance after pelvic bone tumor resection and important complications including infection, tumor recurrence, and complications related to complex soft tissue and osseous reconstruction.
Evaluation of different illumination designs for tunable 3D structured illumination microscopy through model-based restoration

In a tunable 3D structured illumination microscopy (3D-SIM) based on an illumination system comprised by a multi-slit array and a Fresnel biprism, the 3D structured illumination (SI) pattern depends on the design of the slit array. Previous work studied the impact of the illumination pattern design on the achieved extension of the compact support of the tunable 3D-SIM optical transfer function. In this contribution, we use simulations with different illumination designs that utilize a different number of slits, to evaluate system performance by investigating the lateral and axial resolution achieved in the restored images computed with a regularized iterative 3D model-based algorithm, which minimizes the mean square error between the model and data. Three illumination designs are investigated in which the number of slits is N = 3, 9 and 11 while the corresponding distance between the slits is x0 = 488 μm, 122 μm and 100 μm, respectively. A 3D star-like object, commonly used in resolution analysis of imaging systems, is used in the simulations. Results are quantified using the mean square error and the structured similarity index as well as intensity profiles that show the achieved resolution and robustness to noise in each case. The lateral and axial 3D-SIM theoretical resolution limits are achieved in the presence of 20-dB Poisson noise while small differences are evident in the results from 15-dB simulated data obtained using the 3 investigated designs.
Handbook of Minerals as Nutritional Supplements

Calcium Overview of Function and Metabolism Status Assessment Methodology Bioavailability of Different Supplements Typical Intakes Versus Needs Current Research on Supplement Uses Toxicity Issues Magnesium Overview of Function and Metabolism Status Assessment Methodology Bioavailability of Different Supplements Typical Intakes Versus Needs Current Research on Supplement Uses Toxicity Issues Potassium Overview of Function and Metabolism Status Assessment Methodology Bioavailability of Different Supplements Typical Intakes Versus Needs Current Research on Supplement Uses Toxicity Issues Iron Overview of Function and Metabolism Status Assessment Methodology Bioavailability of Different Supplements Typical Intakes Versus Needs Current Research on Supplement Uses Toxicity Issues Zinc Overview of Function and Metabolism Status Assessment Methodology Bioavailability of Different Supplements Typical Intakes Versus Needs Current Research on Supplement Uses Toxicity Issues Copper Overview of Function and Metabolism Status Assessment Methodology Bioavailability of Different Supplements Typical Intakes Versus Needs Current Research on Supplement Uses Toxicity Issues Selenium Overview of Function and Metabolism Status Assessment Methodology Bioavailability of Different Supplements Typical Intakes Versus Needs Current Research on Supplement Uses Toxicity Issues Manganese Overview of Function and Metabolism Status Assessment Methodology Bioavailability of Different Supplements Typical Intakes Versus Needs Current Research on Supplement Uses Toxicity Issues Chromium Overview of Function and Metabolism Status Assessment Methodology Bioavailability of Different Supplements Typical Intakes Versus Needs Current Research on Supplement Uses Toxicity Issues Others Overview of Function and Metabolism Status Assessment Methodology Bioavailability of Different Supplements Typical Intakes Versus Needs Current Research on Supplement Uses Toxicity Issues
Adenosine 3':5'-monophosphate-dependent protein kinase and the stimulation of ovarian nuclear ribonucleic acid polymerase activities.

Abstract The cyclic adenosine 3':5'-monophosphate-dependent (cyclic AMP-dependent) protein kinase of calf ovary cytosol has been partially purified and characterized. This preparation activated and possibly phosphorylates ovarian nuclear RNA polymerases Ia, Ib, and II. Cyclic AMP-dependent protein kinase of calf ovary cytosol has been dissociated into a cyclic AMP-binding protein subunit and into a cyclic AMP-independent protein kinase subunit. Isolation of the cyclic AMP-binding protein and of the cyclic AMP-independent protein kinase resulted in a 110-fold purification of both sub-units. The cyclic AMP-independent protein kinase used histone F1, protamine, phosvitin, casein, and Escherichia coli RNA polymerase as substrates and appeared to exhibit little substrate specificity. The apparent Km value of the cyclic AMP-independent protein kinase for ATP was determined as 1.8 x 10-5 m. The cyclic AMP-binding protein was determined by Sephadex gel filtration to have a molecular weight of about 135,000. The molecular weight of the cyclic AMP-independent protein kinase was estimated to be in the range of about 375,000. Dissociation of the cyclic AMP-independent protein kinase by sodium dodecyl sulfate resulted in the formation of three subunits exhibiting molecular weights of 26,000, 64,000, and 90,000, respectively. The cyclic AMP-dependent protein kinase in the presence of 5 x 10-9 m cyclic AMP, and the cyclic AMP-independent protein kinase stimulated the incorporation of 32P from [γ-32P] ATP into fractions containing nuclear RNA polymerases Ia, Ib, and II. Chromatography on DEAE-cellulose indicated a coincidence of the phosphorylated proteins with the three polymerase activities but no proof of the incorporating of 32P into the RNA polymerases themselves has yet been provided. The fraction containing RNA polymerase II activity was the preferred substrate as judged by the significantly higher incorporation of 32P. The cyclic AMP-dependent phosphorylation of the RNA polymerase preparations was associated with an increase of the RNA-synthesizing activity of all three enzyme preparations. The activity of the polymerase II was increased 9-fold after phosphorylation. Only a 2.5- to 3-fold stimulation of RNA synthesis by the phosphorylated polymerases Ia and Ib was observed. These results suggest that cyclic AMP and protein kinase play an important role in the hormonal control of ovarian nuclear RNA synthesis through regulation and perhaps phosphorylative modification of the ovarian nuclear RNA polymerases.
Recent Studies of the Metabolism of Abscisic Acid

Abscisic acid is the only one of the five major plant growth substances of which the biosynthetic pathway in higher plants remains unknown. In fungi, there is good evidence that the direct pathway from MVA via farnesyl pyrophosphate operates, with α- or γ-ionylidene derivatives as intermediates in the later stages of the pathway [26]. On the other hand, there is considerable evidence that in higher plants ABA is synthesized via the indirect pathway in which ABA is a breakdown product of a larger precursor molecule, probably a carotenoid [26]. Results of 18O2 labeling studies of ABA produced in water-stressed leaves strongly favor the indirect pathway. In this paper we report on recent investigations of 18O incorporation into ABA from stressed as well as from non-stressed tissues.
DOES OUR DNA DETERMINE WHEN WE SLEEP

The discovery and study of three kindreds with advanced sleep phase disorder shed light on how we can inherit tendencies to be early morning or late night kinds of people ( pages 1062–1065 ).
Triblock copolymer ionomer membranes Part II. Structure characterization and its effects on transport properties and direct methanol fuel cell performance

Abstract In this study, the morphology, transport properties, selectivity, and direct methanol fuel cell (DMFC) performance of a triblock copolymer ionomer, sulfonated poly(styrene–isobutylene–styrene) (S-SIBS), were investigated. The structure of S-SIBS membranes, ranging from 0.5 to 1.0 meq/g, was characterized using small-angle X-ray scattering and revealed a lamellar morphology with a preferred orientation in the plane of the membrane. Subsequently, proton conductivity measured normal to the plane of the membrane was over 10 times lower than when measured in plane , compared to only a 2.5 times difference in conductivity between the two techniques in Nafion 117. When proton conductivity was measured normal to the plane , the resulting selectivities (i.e. proton conductivity/methanol permeability) of S-SIBS membranes are similar to Nafion 117. A previous study [J. Membrane Sci. 217 (2003) 227] reports 5–10 times higher selectivities compared to Nafion 117 when conductivities were measured in plane . In addition, the DMFC performance of S-SIBS (1.0 meq/g) was lower than that of Nafion 117. These significant differences in transport properties and fuel cell performance with respect to polymer structure in S-SIBS membranes provide new insights into designing oriented nanostructures in polymer electrolyte membranes for enhanced transport properties for fuel cell applications.
Modifications of the Normal Equations Method that are Numerically Stable

A method of solving min ∥ b − Ax ∥ where A is an m × n matrix is presented which appears to be as stable as methods based on orthogonal factorization but in certain cases is nearly as efficient as methods based on factoring the normal equations. Iterative refinement is used in the new method. Also a class of methods is described that in terms of efficiency (for m ≥ 2n) and, apparently, numerical stability is intermediate between orthogonalization methods and normal equations methods. The class can be considered to be a block implementation of the modified Gram-Schmidt algorithm.
Behavioral Synthesis: an Overview

Behavioral synthesis bridges the gap between abstract specifications and concrete hardware implementations. The behavioral synthesis problem consists of mapping a largely incompletely defined behavior into a well-defined hardware implementation with fixed sequential behavior. This paper presents an overview of the main algorithms and issues related to behavioral synthesis and analyzes the pros and cons of each technique. It also discusses the place for behavioral synthesis in the overall digital design methodology and the main advantages and drawbacks of its use
On certain representations of semi-simple algebraic groups

Suppose that k is an algebraic number field, G a connected semi-simple algebraic group, and ρ a rational representation of G in a vector space X defined over k. The triple (G,X,ρ) or simply ρ is called admissible over k if the Weil criterion [9, p. 20] for the convergence of the integral over G A /G k of the generalized theta-series $$\sum\limits_{\xi \in X_k } {\Phi (\rho (g) \cdot \xi )} $$ is satisfied. (The subscript A denotes the adelization functor relative to k and ϕ is an arbitrary Schwartz-Bruhat function on X A .) It is called absolutely admissible if it is admissible over any finite algebraic extension of k. We shall discuss a complete classification of all absolutely admissible representations. (If G is absolutely simple, there are essentially 6 infinite sequences of, and 26 isolated, absolutely admissible triples.) Then, in the general case, we shall discuss the existence and basic properties of what we call the principal subset X′ of X. Although the adjoint representation of G can never be absolutely admissible, we can say that X′ is analogous to the set of regular elements of the Lie algebra of G via its adjoint representation [cf. 4]. The significance of X′ is that it permits us to formulate a conjectural Siegel formula in a precise, explicit form. (The restriction to X′ corresponds in the classical Siegel case to considering only those terms which contribute to cusp forms.) We shall discuss a weak solution of this conjecture in the general case. Finally, if there exists only one G-invariant, we shall discuss its solution as well as the analytic continuation and the functional equation of the corresponding zeta-function.
Improving seismic resolution of prestack time-migrated data

Seismic resolution significantly affects the quality of seismic interpretation. Processing parameters that effect resolution such as picking velocities in the presence of interbed multiples benefit from an understanding of the underlying geology. Three-dimensional migration is almost always performed by an external service company or internal specialty processing group, with the “final” product being migrated gathers and the final migration-stack section. In the Chicontepec Basin, Mexico, we have evaluated improvements in data quality made after 3D prestack time migration. By first mapping shallow volcanics that generated strong interbed multiples, we performed a new velocity analysis to better image the weaker, underlying primaries of interest. We remove the local migration stretch through an inverse NMO correction, followed by a nonstretch NMO correction and prestack structure-oriented filtering. Such compensation for migration stretch improves the vertical resolution and preserves far-offset data valuable to subsequent prestack inversion that would otherwise need to be muted. Because S-impedance inversion depends heavily on the farther offsets, the resulting S-impedance images have resolution that is in general equivalent to and, in the target area of rapid S-impedance seen in the well logs, exceed that of the P-impedance images. Attributes such as coherence and curvature show improved fault resolution, whereas noisy areas look more chaotic because of the increased frequency content.
Spectroscopic analysis of non-LTE gold plasmas

Summary form only given. Understanding and predicting the characteristics of non-LTE plasmas plays an important role in the development of inertial confinement fusion schemes. This paper presents a preliminary spectroscopic analysis of M-shell gold spectra collected over a wide range of electron and radiation temperatures. The 2.9-4.2 keV emission spectra are obtained from gold samples embedded in beryllium disks that are directly heated by the Omega laser, forming plasmas with electron densities near 10/sup 21/ cm/sup -3/ and electron temperatures from 1 to 3 keV. Some of the disks are placed within hohlraums, providing a finite radiation temperature near 150 eV. The spectra from these plasmas are analyzed to determine the variation of the gold charge state balance over a wide range of plasma conditions. The spectroscopic analysis is complemented by Thomson scattering and imaging of plasma expansion, which provide independent estimates of electron densities and temperatures.
Chronic myelogenous leukemia after lymphoid irradiation and heart transplantation

We have previously reported a case of recurrent cardiac rejection in a heart transplant recipient successfully treated with total lymphoid irradiation. Five years after transplantation chronic myelogenous leukemia was diagnosed in this patient. The long-term effects of total lymphoid irradiation in the heart transplant population have not been reported. Based on the known relationships among irradiation, gene translocations, and leukemia, we postulate that this patient's chronic myelogenous leukemia may be a long-term sequela of previous total lymphoid irradiation.
Contrast-enhanced MR imaging of the liver: comparison between Gd-BOPTA and Mangafodipir.

The purpose of the study was to evaluate the MR contrast agents gadolinium benzyloxypropionictetro-acetate (Gd-BOPTA) and Mangafodipir for liver enhancement and the lesion-liver contrast on T1W spin-echo (SE) and gradient-recalled-echo (GRE) images. Fifty-one patients (three groups of 17 patients each) with known or suspected liver lesions were evaluated with T1W SE (300/12) and GRE (77-80/2.3-2.5/80 degrees) images before and after intravenous (IV) Gd-BOPTA (0.1 or 0.05 mmol/kg) or Mangafodipir (5 mumol/kg) in phase II to III clinical trials. Quantitative analysis by calculating liver signal-to-noise ratio (SNR), lesion-liver contrast-to-noise ratio (CNR), and spleen-liver CNR was performed. Liver SNR and spleen-liver CNR were always significantly increased postcontrast. SNR was highest after application of 0.1 mmol/kg Gd-BOPTA (51.3 +/- 3.6, P < .05). CNR was highest after Mangafodipir (-22.6 +/- 2.7), but this was not significantly different from others (P = .07). Overall, GRE images were superior to SE images for SNR and CNR. Mangafodipir and Gd-BOPTA (0.1 mmol/kg) provide equal liver enhancement and lesion conspicuity postcontrast. By all criteria, contrast-enhanced T1-weighted GRE were comparable to SE images.
Fresnel and refractive lenses for X-rays

Abstract We present a Gaussian beam analysis of X-ray refractive and Fresnel lenses. The X-ray refractive lens is featured by an intrinsic soft (Gaussian) aperture due to strong absorption of X-rays by materials. We defined a parameter N0, the critical Fresnel number (CFN), to describe this optical property. The values of N0 for all practical materials are below 1000 for photon energies exceeding 30 eV, still lower for high-Z materials. The maximum effective Fresnel number of a lens is determined by its material to be 2N0 and its maximum enhancement of X-ray intensity is limited to (2πN0)2, independent of its shape. We found that the refractive lens is likely to be useful for manipulating nearly diffraction limited beam in the hard X-ray region and its application is severely restricted by available fabrication capabilities today. X-ray Fresnel lenses, both in cylindrical and linear forms, are proposed as superior focusing elements for hard X-rays. Their high efficiency, up to 100% in optimal construction, will enable us to manipulate beams with multiple lenses and obtain higher performance optics. Their design and fabrication are discussed in reference to those of X-ray Fresnel zone plates and micro Fresnel lenses for optoelectronics.
Making Meaning of Urban American Indian Identity: A Multistage Integrative Process

The cultural identity and tribal connectedness of American Indians are commonly believed to have been negatively affected by the urbanization process in which American Indians have been involved during the past half century. This phenomenological study examined the processes through which cultural identity was formed and maintained by a group of American Indians who had lived since childhood in urban areas, away from their reservations or tribal communities. Seven urban Indian adults, each from a different tribe, shared their experiences related to coming to understand what it means to be American Indian and the development of their American Indian cultural identity. Four themes emerged from participant interviews and were seen to correspond to stages that participants passed through, from their teens through their 30s, that led to understanding and integration of their American Indian identity. Findings point to the importance of considering issues of cultural identity development when providing social work services to urban American Indian young adults.
Study of Placing a Second Intravenous Line in Trauma

AbstractObjective. We evaluated the benefit of emergency medical services providers’ placing a second intravenous (IV) line in the prehospital trauma setting. Our hypothesis was that the placement of a second IV catheter in trauma does not result in an improvement in heart rate, blood pressure, rehospitalizaton rate, or 30-day mortality. Methods. A retrospective chart review of 320 trauma patients in a one-year period was conducted at our level I trauma center. All trauma patients who had vascular access obtained prehospitally were included. Results. Patients with two IV lines received an average of 348.4 mL more fluid (95% confidence interval [CI]: 235.6, 461.1; p < 0.0001). No change in heart rate, pulse oximetry, Glasgow Coma Scale score, systolic blood pressure, rehospitalization rate, or 30-day mortality was noted. These effects persisted for patients who were initially tachycardic (heart rate 3.92 bpm; 95% CI –3.01, 10.82; p = 0.27) or hypotensive (blood pressure 22.00 mmHg; 95% CI −4.17, 48.16; p =...
Paraphyly, ancestors, and the goals of taxonomy: A botanical defense of cladism

Cronquist (1987) criticizes cladism for its rejection of paraphyletic groups, which he would retain if he feels they are “conceptually useful.” We argue that paraphyletic higher taxa are artificial classes created by taxonomists who wish to emphasize particular characters or phenetic “gaps,” and that formal recognition of such taxa conveys a misleading picture of common ancestry and character evolution. In our view, classifications should accurately reflect the nested hierarchy of monophyletic groups that is the natural outcome of the evolutionary process. Such systems facilitate the study of evolution and provide an efficient summary of character distributions. Paraphyletic groups, such as “prokaryotes,” “green algae,” “bryophytes,” and “gymnosperms,” should be abandoned, as continued recognition of such groups will only serve to retard progress in understanding evolution. Contrary to Cronquist’s (1987) assertions, cladistic theory is not at odds with standard views on speciation and the existence of ancestors. Groups of interbreeding organisms can continue to exist after giving rise to descendant species, and there are several ways in which such groups, whether extant or extinct, can be incorporated into cladistic classification. In contrast, paraphyletic higher taxa are neither cohesive (integrated by gene flow) nor whole, do not serve as ancestors, and are unacceptable in the phylogenetic system. Fossils may be of great value in assessing phylogenetic relationships and are readily accommodated in cladistic classification. Cladistic studies are helping to answer major questions about plant evolution, and we anticipate increased efforts to develop a truly phylogenetic system.
Coexistence of superconductivity and long-range antiferromagnetic order in the compound ErxMo6Se8

Abstract Low temperature specific heat and magnetic susceptibility measurements indicate that superconductivity and long-range antiferromagnetic order coexist in the compound Er x Mo 6 Se 8 ( x = 1.0 and 1.2).
Visual research, evaluation and assessment in the age of computer graphics

Often, I get some of my best ideas in the morning, when it's quiet, closing my eyes and envisioning my thoughts. By the time I've had my coffee and ready to walk out the door, they may not be as apparent, if at all. If I were hardwired to a computer, my thoughts could be reviewed and analyzed, adding an additional dimension to assessing their applicable value.Though it may not be currently possible to store and retrieve actual thoughts from a hard drive, content that is stored and retrievable is derived through a conscious thought process. Computer graphics applications allow for a visual analysis of the data for use in multiple areas. This issue takes up four.
Building Skills in Thinking: Toward a Pedagogy in Metathinking.

Most managers do not receive formal training in metathinking—that is, they are not trained formally in thinking about thinking or in thinking about deciding. In this article, the authors review the lack of educational focus on metathinking and suggest several tools for improving the decision-making process and for skill building in metathinking. The tools include two experiential exercises that facilitate learning in metathinking.
Loss of cilia suppresses cyst growth in genetic models of autosomal dominant polycystic kidney disease

Stefan Somlo and colleagues show that loss of intact cilia suppresses cyst growth in genetic models of autosomal dominant polycystic kidney disease (ADPKD). They further show that the severity of cystic disease in these models is directly related to the length of time between the initial loss of polycystins and the subsequent involution of cilia, implicating a cilia-dependent cyst growth–promoting pathway in the pathogenesis of ADPKD.
Invariants and state in testing and formal methods

Logical formulas called invariants are a staple of formal methods for program analysis. Persistent-state variables appear in these formulas playing their proper intuitive role, which is somewhere between inputs and internal variables. In software testing theory, on the contrary, state is not usually accorded explicit treatment. Comparing the viewpoints of formal methods and testing theory suggests new roles that formal methods can play in testing. This examination is motivated by recent systems such as Daikon, which use both tests and invariants.
The mixing rate of the arterial blood pressure waveform Markov chain is correlated with shock index during hemorrhage in anesthetized swine

Identifying the need for interventions during hemorrhage is complicated due to physiological compensation mechanisms that can stabilize vital signs until a significant amount of blood loss. Physiological systems providing compensation during hemorrhage affect the arterial blood pressure waveform through changes in dynamics and waveform morphology. We investigated the use of Markov chain analysis of the arterial blood pressure waveform to monitor physiological systems changes during hemorrhage. Continuous arterial blood pressure recordings were made on anesthetized swine (N=7) during a 5 min baseline period and during a slow hemorrhage (10 ml/kg over 30 min). Markov chain analysis was applied to 20 sec arterial blood pressure waveform segments with a sliding window. 20 ranges of arterial blood pressure were defined as states and empirical transition probability matrices were determined for each 20 sec segment. The mixing rate (2(nd) largest eigenvalue of the transition probability matrix) was determined for all segments. A change in the mixing rate from baseline estimates was identified during hemorrhage for each animal (median time of 13 min, ~10% estimated blood volume, with minimum and maximum times of 2 and 33 min, respectively). The mixing rate was found to have an inverse correlation with shock index for all 7 animals (median correlation coefficient of -0.95 with minimum and maximum of -0.98 and -0.58, respectively). The Markov chain mixing rate of arterial blood pressure recordings is a novel potential biomarker for monitoring and understanding physiological systems during hemorrhage.
Amplification of intrinsic fluctuations by chaotic dynamics in physical systems

A quantitative method for the treatment of large-scale intrinsic fluctuations amplified by chaotic trajectories in macrovariable physical systems is presented. Paradigmatic results for the Rossler model and preliminary computational results for chaotic Josephson junctions and for chaotic multimode Nd:YAG (yttrium aluminum garnet) lasers are described. These studies are directed towards identification of a real physical system in which experimental confirmation may be realized. The probability distribution on the intrinsic-noise-modified, chaotic attractor is identified as a likely candidate for comparison of experiment and theory.
Time synchronization attacks in sensor networks

Time synchronization is a critical building block in distributed wireless sensor networks. Because sensor nodes may be severely resource-constrained, traditional time-synchronization protocols cannot be used in sensor networks. Various time-synchronization protocols tailored for such networks have been proposed to solve this problem. However, none of these protocols have been designed with security in mind. If an adversary were able to compromise a node, he might prevent a network from effectively executing certain applications, such as sensing or tracking an object, or he might even disable the network by disrupting a fundamental service such as a TDMA-based channel-sharing scheme. In this paper we give a survey of the most common time synchronization protocols and outline the possible attacks on each protocol. In addition, we discuss how different sensor network applications that are affected by time synchronization attacks, and we propose some countermeasures for these attack.
A Reliable Routing Architecture and Algorithm for NoCs

Aggressive transistor scaling continues to drive increasingly complex digital designs. The large number of transistors available today enables the development of chip multiprocessors that include many cores on one die communicating through an on-chip interconnect. As the number of cores increases, scalable communication platforms, such as networks-on-chip (NoCs), have become more popular. However, as the sole communication medium, these interconnects are a single point of failure so that any permanent fault in the NoC can cause the entire system to fail. Compounding the problem, transistors have become increasingly susceptible to wear-out related failures as their critical dimensions shrink. As a result, the on-chip network has become a critically exposed unit that must be protected. To this end, we present Vicis, a fault-tolerant architecture and companion routing protocol that is robust to a large number of permanent failures, allowing communication to continue in the face of permanent transistor failures. Vicis makes use of a two-level approach. First, it attempts to work around errors within a router by leveraging reconfigurable architectural components. Second, when faults within a router disable a link's connectivity, or even an entire router, Vicis reroutes around the faulty node or link with a novel, distributed routing algorithm for meshes and tori. Tolerating permanent faults in both the router components and the reliability hardware itself, Vicis enables graceful performance degradation of networks-on-chip.
Is there a Definition of Remission in Late-Life Depression that Predicts Later Relapse?

Remission of depressive symptoms is the goal of all antidepressant therapy. Rating scales define remission in clinical trials, but it is unclear how well these definitions predict risk of later relapse. We measured the sensitivity and specificity of a range of Montgomery–Asberg Depression Rating Scale (MADRS) cutoff scores at 3- and 6-months, wherein scores above a given cutoff would predict relapse over an 18-month period. We examined 153 elderly depressed subjects exhibiting a MADRS ⩽15 after 3 or 6 months of antidepressant therapy. Subjects who subsequently exhibited a MADRS >15 during the 18-month study period were defined as relapsed. Receiver operating characteristic (ROC) curves were developed and area under the curve (AUC) values calculated for the sensitivity and specificity of 3- and 6-month MADRS scores to predict future relapse. The 3-month ROC had an AUC value of 0.63; the 6-month ROC had an AUC value of 0.66. There was no MADRS cutoff found that could predict likelihood of relapse with good sensitivity and specificity. A post hoc analysis where relapse rate was adjusted by controlling for medical comorbidity, disability, and social support showed no change in the ROCs or AUC values. The higher the MADRS score at 3 and 6 months, the greater the likelihood of relapse. With no clean MADRS cutoff score, the goal of antidepressant therapy should be the lowest possible degree of depressive symptomatology to minimize risk of later relapse. Definitions of remission that are better associated with longer-term outcomes are needed.
Influence of propranolol, phenoxybenzamine or phentolamine on the in vivo nocturnal rise of pineal melatonin levels in the syrian hamster

Abstract In the Syrian hamster, pineal melatonin levels exhibit a 15-fold rise during the dark phase of the light: dark cycle. This rise is believed to be mediated by the release of norepinephrine from the postganglionic sympathetic fibers which terminate within the pineal. In order to determine the nature of the adrenergic receptor involved in the norepinephrine mediated nocturnal increase in melatonin, male hamsters were treated with either α- or β-adrenergic blockers just prior to lights out. Subsequently, radioimmunoassayable levels of melatonin were measured at 7, 8 and 9 hours (0300, 0400 and 0500 h, respectively) into the dark period. Propranolol (20 mg/kg) completely suppressed the nocturnal rise of melatonin while phentolamine (10 mg/kg) had no effect upon the increase. The minimum amount of propranolol necessary to block the nighttime rise of melatonin was determined to lie between 1 mg/kg and 10 mg/kg. Phenoxybenzamine (20 mg/kg) exhibited a slight, although statistically significant, blockade of the nocturnal melatonin rise.
Integrated and individual biochemical responses of rainbow trout (Salmo gairdneri) to varying durations of acidification stress

Abstract 1. Rainbow trout displayed a variety of biochemical responses when exposed to pH 4.5 for periods of 6–48 hr. 2. Some adaptive or recovery responses occur in rainbow trout after 12–24hr of continuous exposure to reduced pH, with most biochemical variables returning to near control levels following 48 hr of nonexposure. 3. The integrated biochemical response of trout to acidification stress was determined by incorporating all 10 measured biochemical variables into a discriminant analysis procedure. 4. Measures of electrolyte homeostasis (sodium), carbohydrate metabolism (glucose), lipid metabolism (triglycoride) and amino acid metabolism (serum glutamate oxaloacetate transaminase) provide the best indicators of individual biochemical responses of trout to reduced pH. 5. Determination and interpretation of fish response to reduced pH can differ, depending on whether individual or multiple biochemical variables are being evaluated.
23Na-NMR studies of Na+ interaction with human red cell membranes from normotensives and hypertensives

Na+ interaction with unsealed human red cell ghosts has been studied by 23Na-NMR relaxation rate (R1) measurements. Data on a total of nine subjects including seven volunteer normotensives (NBP) and two untreated hypertensives (HBP) are presented. Qualitative treatment of the data gives information on the dynamic behavior of Na+ undergoing fast exchange between the free and bound states. The excess longitudinal relaxation rate (ΔR)−1 plotted against total [Na+], known as the James-Noggle plot, exhibits different behavior for NBP and HBP ghosts, with a relatively low binding constant of approx. 100 M−1 for HBP (p<0.025) compared to a high constant of 500–1000 M−1 for NBP. To associate our NMR data with membrane-bound (Na++K+)-ATPase, 23Na relaxation rates were measured in the presence of 5 mM ouabain. James-Noggle plots constructed for ouabain-sensitive excess relaxation rates show the binding for NBP to be even high affinity (103 M−1) but low capacity. These data may suggest that for a given amount of intracellular Na+, the binding affinity could determine the distribution of Na+ between the membrane and cytoplasm, and that the (Na++ K+) -ATPase which is primarily responsible for the Na+ affinity might assume an abnormal transport mechanism in HBP membranes.
5-HT3 receptors are membrane ion channels

The neurohormone 5-hydroxytryptamine (5HT or serotonin) exerts its effects by binding to several distinct receptors. One of these is the M-receptor of Gaddum and Picarelli, now called the 5-HT3 receptor, through which 5-HT acts to excite enteric neurons. Ligand-binding and functional studies have shown that the 5-HT3 receptor is widely distributed in peripheral and central nervous tissue and evidence suggests that the receptor might incorporate an ion channel permeable to cations. We now report the first recordings of currents through single ion channels activated by 5-HT3 receptors, in excised (outside-out) membrane patches from neurons of the guinea pig submucous plexus. Whereas application of acetylcholine activated predominantly a 40-pS channel, 5-HT caused unitary currents apparently through two channels of conductances of 15 and 9 pS, which were reversibly blocked by antagonists of the 5-HT3 receptor. Receptors for amine neurotransmitters, including 5-HT1 and 5-HT2, have previously been thought to transduce their effects through GTP-binding proteins: the direct demonstration that 5-HT3 receptors are ligand-gated ion channels implies a role for 5-HT, and perhaps other amines, as a 'fast' synaptic transmitter.
Meaning in Speech and in Thought

If we think in a lingua mentis, questions about relations between linguistic meaning and propositional-attitude content become questions about relations between meaning in a public language (p-meaning) and meaning in a language of thought (t-meaning). Whether or not the neo-Gricean is correct that p-meaning can be defined in terms of t-meaning and then t-meaning defined in terms of the causal-functional roles of mentalese expressions, it's apt to seem obvious that separate accounts are needed of p-meaning and t-meaning, since p-meaning, unlike t-meaning, must be understood at least partly in terms of communication. Paul Horwich, however, claims that his ‘use theory of meaning’ provides a uniform account of all meaning in terms of ‘acceptance properties’ that, surprisingly, implicate nothing about use in communication. But it turns out that the details of his theory belie his claim about it.
Europium Oxychloride Absorption Spectroscopy as an Optical Probe of Temperature

Abstract The temperature dependence of the features which arise from the 7F0,1 → 5D3 absorption transitions in EuOCl as seen by diffuse-reflectance spectroscopy has been investigated. The transitions shift linearly to higher energy with increasing temperature. The ratio of the intensities of the transitions arising from the 7F0 state to those arising from the 7F1 state also appears to be a linear function of temperature.
The coat protein subunits of cucumber viruses 3 and 4 and a comparison of methods for determining their molecular weights

Abstract Chemical analyses (amino acid composition coupled with peptide mapping), gel chromatography and SDS-polyacrylamide gel electrophoresis were used to determine the molecular weights of the coat protein subunits of several strains of cucumber viruses 3 and 4 (CV3 and CV4). The results obtained by means of amino acid analyses and peptide mapping were 17,100 for two strains of CV3 and 16,100 for two strains of CV4. These values are considered accurate to within ±1%, and if they are considered to be the actual values, the results obtained on these same strains of CV3 and CV4 by C-terminal analyses, SDS-polyacrylamide gel electrophoresis, and gel chromatography show deviations ranging from −0.6% to +47%. Gel chromatography in guanidine hydrochloride appeared to be next in reliability to amino acid analyses and peptide mapping.
Envelope–Receptor Interactions in Nipah Virus Pathobiology

Nipah (NiV) and Hendra (HeV) viruses are members of the newly defined Henipavirus genus of the Paramyxoviridae. Nipah virus (NiV) is an emergent paramyxovirus that causes fatal encephalitis in up to 70% of infected patients, and there is increasing evidence of human-to-human transmission. NiV is designated a priority pathogen in the NIAID Biodefense Research Agenda, and could be a devastating agent of agrobioterrorism if used against the pig farming industry. Endothelial syncytium is a pathognomonic feature of NiV infections, and is mediated by the fusion (F) and attachment (G) envelope glycoproteins. This review summarizes what is known about the pathophysiology of NiV infections, and documents the identification of the NiV receptor. EphrinB2, the NiV and HeV receptor, is expressed on endothelial cells and neurons, consistent with the known cellular tropism for NiV. We discuss how the identification of the henipahvirus receptor sheds light on the pathobiology of NiV infection, and how it will spur the rational development of effective therapeutics. In addition, ephrinB3, a related protein, can serve as an alternative receptor, and we suggest that differential usage of ephrinB2 versus B3 may explain the variant pathogenic profiles observed between NiV and HeV. Thus, identifying the NiV receptors opens the door for a more comprehensive analysis of the envelope-receptor interactions in NiV pathobiology. Finally, we also describe how galectin-1 (an innate immune defense lectin) can interact with specific N-glycans on the Nipah envelope fusion protein, underscoring the potential role that innate immune defense mechanisms may play against emerging pathogens.
Interactions Between a Canard and Thick Bodies: Analysis and Applications

A modular model, consisting of cruciform canard controls mounted on a thin forebody and e ve interchangeable thick (larger-diameter ) main bodies, was tested at a Mach number of 0.8. The canard was installed at the + + and x positions and at dee ection angles of 0, 6, and 12 deg. The model was equipped with two sting balances in a setup that enabled to obtain theloads acting on thecanard unitand those acting on themain bodies. Fourinteractionson mainbody normalforceandcenterofpressureareidentie edand quantie ed:effectsofthecanard on thethickening of the main bodies and on the boattails, as a function of angle of attack and canard dee ection. The interactions are analyzed using an approximate vortex tracker, which is based on slender body theory. Then, the pertinent part of the Pitts, Nielsen, and Kaattari component buildup method is used to calculate the interactions. The results of the analysis are in good agreement with the present test data, except for the effect of canard dee ection on the boattail, where the analysis leaves a large gap. Using the present method, to add the subject effects to component buildup analysis of variety of cone gurations improves the agreement with test data.