cssi/SciSciGPT-SciSciNet huggingface dataset:
Immunoaffinity Purification and Structural Analysis of Human Breast Cancer Progesterone Receptors

Progesterone receptors (PR) are well established as an important clinical marker in breast cancer in predicting patient response to adjuvant endocrine therapies1 and as markers of disease aggressiveness.2 Development of antibodies specific for human PR and methods for their use in the immunocytochemical detection of receptors in breast tumors would be of value clinically in providing a number of advantages over the biochemical ligand binding assays that are currently in use for routine PR determinations. Immunocytochemistry for example, will make PR screening accessible to most pathology laboratories, is possible to perform with cellular aspirates and very small tissue samples, and will provide information on cellular heterogeneity and PR content in individual cells which itself may be of diagnostic value.
4-dimensional, multiphase, steady-state imaging with contrast enhancement (MUSIC) in the heart; a feasibility study in children

Background Conventional breath-held gadolinium-based contrastenhanced MR angiography (CE-MRA) provides excellent definition of extra-cardiac anatomy, but does not provide diagnostic image quality for intra-cardiac anatomy because it is not gated to ECG due to time constraints associated with breath-holding and the need to capture the first-pass of gadolinium. To address this issue, we propose a 4D non-breath-held multiphase steady-state imaging sequence (MUSIC) using ferumoxytol, which is an FDA approved iron-oxide particle for treating irondeficiency anemia, as an intravascular contrast agent and demonstrate its feasibility in children with congenital heart disease (CHD).
7-Tesla MRI of the brain in a research subject with bilateral, total knee replacement implants: Case report and proposed safety guidelines.

Abstract Recently, the first 7-T MR system was approved for clinical use in the United States. Unfortunately, relatively few metallic implants have undergone testing to determine if they are acceptable or pose hazards to research subjects and patients at this ultra-high-field strength. Therefore, in lieu of not performing a research or clinical MRI exam at 7-T, the supervising physician may make a decision to scan the individual with an untested metallic implant based on an analysis of the risks vs. the benefits. We present a case report of a research subject with bilateral, total knee replacement implants that safely underwent MRI of the brain at 7-T and provide guidelines for healthcare professionals to follow in order to ensure safety in research subjects or patients with metallic implants referred for 7-T scans.
Assessing Barriers to Uveitis Screening in Patients with Juvenile Idiopathic Arthritis Through Semi-Structured Interviews.

Introduction Uveitis is a significant complication in patients with juvenile idiopathic arthritis (JIA) and can be asymptomatic until vision loss develops. Published guidelines recommend uveitis screening eye examinations every 3-12 months depending on multiple factors, but no literature evaluates adherence with and barriers to obtaining these screening eye examinations. This study assesses barriers in nonadherent patients to establish key drivers for future interventions. Methods We identified patients with JIA who were nonadherent with uveitis screening guidelines through the electronic medical record (EMR). A rheumatologist conducted semistructured interviews with the patients or guardians regarding the patients' most recent eye examinations, knowledge of the screening frequency, and barriers to completing the eye examinations. The results were qualitatively analyzed to determine any categorical variables present. Results Ninety-two patients were identified as nonadherent, and the rheumatologist interviewed 45 patients or guardians. Categories identified following the interviews were system problems, access to care issues, and knowledge deficits. The largest category identified was system problems that included most recent eye examination not being in the EMR, the wrong eye provider identified in the EMR or difficulty with scheduling eye appointments. Conclusions This qualitative study identified categories of barriers to obtaining screening eye examinations in patients with JIA. Identification of these barriers will facilitate the development of a specific aim and key driver diagram to guide future quality improvement interventions.
Selective enzymatic amplification of alpha 2-globin DNA for detection of the hemoglobin Constant Spring mutation.

Hemoglobin Constant Spring is an elongation mutation of the alpha 2- globin locus that results in a thalassemic phenotype. It has a high prevalence in Asian populations. When inherited with other alpha- thalassemia determinants, the Constant Spring gene has the potential to cause severe forms of alpha-thalassemia. Accurate diagnosis of the condition with standard hemoglobin electrophoresis is unreliable due to the small to undetectable amounts of the mutant hemoglobin present. Because of the extensive sequence homology of the alpha 1 and alpha 2 loci, allele-specific hybridization to total genomic DNA containing the Constant Spring gene would not distinguish between heterozygous and homozygous hemoglobin Constant Spring. Selective enzymatic amplification of alpha 2-globin DNA sequences, however, allows unambiguous diagnoses to be made using allele-specific hybridization. This method is useful for providing accurate genetic counseling and prenatal diagnosis in populations and specific families in which precise diagnosis is important.
Memorial space and its mnemonic function

In this article, I argue that the meaning of memorial space can be better understood by turning our focus to the ambient characteristics of these spaces. Ambience is used here to refer to the envir...
Matthew effects in writing productivity during second grade

The primary aims of this study were twofold: (a) to describe average change in the written narrative performance of second grade students from the fall and spring of the school year and (b) examine patterns of individual growth to test for Matthew effects. Participants included 299 children in second grade. Microstructural measures were derived from students’ written narratives including: number of different words (NDW), total number of words (TNW), and accuracy of spelling and grammar. Significant increases in NDW, TNW, and spelling accuracy were evidenced from fall to spring. Students averaged 55 total words in the fall and averaged 69 words in the spring, with a statistically significant increase of 14 words t(299) = 8.4, p < .0001). The variance in TNW from fall to spring increased from Var = 791 to Var = 1005, which was a significant increase and the correlation of initial Fall TNW and growth in TNW was also significant (r = 0.39). Additionally, results from a two-level hierarchical linear model with students nested within teachers indicated that initial level of TNW predicted the change in TNW from fall to spring, with higher levels of initial TNW being related to larger gains in TNW. Significant predictors of Matthew effects included teacher or classroom and free/reduced lunch eligibility. Written personal narrative measures are sensitive to developmental change across a school year. Evidence of Matthew effects in lexical productivity suggests additional support may be warranted to ameliorate gaps in writing achievement.
Techniques for Mitral Valve Repair

Myxomatous degeneration of mitral valve apparatus affects 2–3% of the general population and it is the most common cause of severe mitral regurgitation in western countries. More than 90% of degenerative mitral valves are suitable for valve repair rather than replacement, with short and long term clinical outcomes being superior after repair. In addition to the clinical benefits, mitral valve repair is associated with an economic benefit in the form of reduced short and long term medical expenses. Patients who have undergone mitral valve repair have mitral function restored, have avoided the added expense of a prosthetic valve and are free from lifelong anti-coagulation requirement. A variety of surgical approaches (sternotomy, anterolateral thoracotomy, and robotic assisted procedures) and repair techniques have been developed over the last four decades to treat mitral valve regurgitation. In this chapter, we delineate different aspects of mitral valve repair techniques.
Unique, Additive, and Interactive Effects of Types of Intimate Partner Cybervictimization on Depression in Hispanic Emerging Adults:

The advent of modern technology has inadvertently created newer avenues for intimate partner victimization (IPV) to transpire. This study investigated (a) whether psychological, sexual, and stalking intimate partner cybervictimization (cyber IPV) types were uniquely associated with depression and whether there were (b) additive and (c) interactive effects of cyber IPV types on depression, after controlling for face-to-face IPV among Hispanic emerging adults. Participants were 903 Hispanic emerging adults in the age range of 18 to 29 years (M = 20.68, SD = 2.42; 74% female) attending a public university in South Texas. Participants completed an online questionnaire assessing cyber IPV types (psychological, sexual, and stalking), face-to-face IPV types (physical, psychological, and sexual), and depression. Results indicated that nearly three-fourths (73%) of the sample endorsed at least one type of cyber IPV. Hierarchical regression analysis showed that psychological and sexual cyber IPV was uniquely associated with depression. An accumulating effect (additive effect model) of the three types of cyber IPV on depression was also found. Interaction effect model analysis yielded no significant effects. Findings reveal the detrimental effect of cyber IPV on mental health and calls for institutions and clinicians to develop preventive and treatment programs to aid victim-survivors.
Adrenocortical hormone in the treatment of pediatric epilepsy

Adrenocortical hormone (ACH) has been used in the treatment of the epilepsies,especially for epileptic encephalopathy,for over 70 years.ACH is clearly established as fast line treatment of infantile spasm and the Landau-Kleffner syndrome.This is typically as monotherapy in infantile spasm,but often in conjunction with anti-epileptic drugs in Landau-Kleffner syndrome,though the mechanism of ACH for epilepsies is not clear.However,in view of these potential adverse side effects,the use of ACH in the treatment of the epilepsies in children must be determined on a risk-benefit basis. Key words: Adrenocortical hormone ; Epilepsy; Children
Implications and Constraints of Time-Independent Poisson Ratios in Linear Isotropic and Anisotropic Viscoelasticity

It is proven that time-independent viscoelastic Poisson ratios (PR) can only exist under separation of variable solutions which severely limits the class of applicable problems to quasi-static ones with incompressible homogeneous materials and non-moving boundaries under separable stress or displacement boundary conditions without any thermal expansions. Therefore, composites which are inherently anisotropic and sandwich structures which are nonhomogeneous and anisotropic are generally precluded from having time-independent PRs. Equal time variations for material properties in all directions are shown to be another simultaneous requirement instead of the incompressibility condition for achieving time-independent PRs. However, such restricted models lead to physically unrealistic bulk moduli responses when compared to experimentally determined relaxation moduli and are not generally achievable in current real materials. Consequently, viscoelastic materials are best characterized in terms of relaxation or creep functions, moduli or compliances rather than combinations of the latter with Poisson's ratios. Additionally, the assumption of constant PRs in problems involving thermal and chemical expansions, such as curing and manufacture of viscoelastic composites, is shown to be unjustified and insupportable. The distinct viscoelastic PR definitions, as found in the literature, are examined and classified into five categories. It is further shown that each is inherently unrelated to the others and all are always time-dependent, unless the above extremely limiting conditions are imposed. An extensive literature review indicates that experimental results overwhelmingly confirm the time dependent nature of viscoelastic PRs as no constant experimentally observed PRs were reported.
Light chain amyloidosis presenting as retiform purpura.

Retiform purpura is a cutaneous sign indicative of vascular damage leading to ischemia, purpura, and necrosis.1 Dermal vascular compromise occurs because of damage of the endothelium or occlusion of the vessel lumen. Herein, we present a patient with retiform purpura, found to have immunoglobulin light chain amyloidosis.
Tail Autotomy Alters Prey Capture Performance and Kinematics, but not Success, in Banded Geckos.

Tails are versatile structures with diverse forms and functions across vertebrates. They are involved in almost all behaviors critical to survival including locomotion, feeding, and predator avoidance. Although the tail's role in locomotion and stability has been widely studied, its role in prey capture is relatively unknown. Lizards are an ideal system to examine the tail's impact on prey capture as most are capable of autotomizing, or dropping, their tail in response to predation and intraspecific competition. Tail autotomy can lower reproduction, decrease locomotor performance, impart instability during jumping, and decrease social status. Desert banded geckos (Coleonyx variegatus) frequently capture evasive prey in nature and appear to use their tail during strikes. However, it is unclear if these tail movements are important for the strike itself, or if they simply draw attention to that part of the body. We used high-speed 3D videography to quantify prey capture performance and kinematics of C. variegatus striking at crickets before and after total caudal autotomy. Trials were conducted within two hours of autotomy and then repeatedly over a two-week period. Overall prey capture success was unaffected by caudal autotomy. However, maximum strike velocity decreased significantly after autotomy, highlighting the importance of the tail during prey capture. Strike kinematics were altered after autotomy in several ways, including geckos adopting a more sprawled posture. Maximum pectoral girdle and mid-back height were significantly lower during post-autotomy strikes, whereas maximum pelvic girdle height was unaffected. However, individual variation was considerable. This downward pitching of the body after tail loss suggests that the tail is necessary for counterbalancing the anterior portion of the body and resisting the rotational inertia incurred after pushing off with the hindlimbs. Utilizing autotomy to test tail function in prey capture can provide valuable insight into how the tail is used in terrestrial predation across a wide variety of species and ecological niches.
ACVR1R206H increases osteogenic/ECM gene expression and impairs myofiber formation in human skeletal muscle stem cells

Abnormalities in skeletal muscle repair lead to poor function and complications such as scarring or heterotopic ossification (HO). Here, we use fibrodysplasia ossificans progressiva (FOP), a disease of progressive HO caused by ACVR1R206H (Activin receptor type-1 receptor) mutation, to elucidate how ACVR1 affects skeletal muscle repair. Rare and unique primary FOP human muscle stem cells (Hu-MuSCs) isolated from cadaveric skeletal muscle demonstrated increased ECM marker expression, and showed skeletal muscle-specific impaired engraftment and regeneration ability. Human induced pluripotent stem cell (iPSC)-derived muscle stem/progenitor cells (iMPCs) Single cell transcriptome analyses from FOP also revealed unusually increased ECM and osteogenic marker expression compared to control iMPCs. These results show that iMPCs can recapitulate many aspects of Hu-MuSCs for detailed in vitro study, that ACVR1 is a key regulator of Hu-MuSC function and skeletal muscle repair; and that ACVR1 activation in iMPCs or Hu-MuSCs contributes to HO by changing the local tissue environment.
Power Factor Estimation of Distributed Energy Resources Using Voltage Magnitude Measurements

This paper presents a new method for the estimation of the injection state and power factor of distributed energy resources (DERs) using voltage magnitude measurements only. A physics-based linear model is used to develop estimation heuristics for net injections of real and reactive power at a set of buses under study, allowing a distribution engineer to form a robust estimate for the operating state and the power factor of the DER at those buses. The method demonstrates and exploits a mathematical distinction between the voltage sensitivity signatures of real and reactive power injections for a fixed power system model. Case studies on various test feeders for a model of the distribution circuit and statistical analyses are presented to demonstrate the validity of the estimation method. The results of this paper can be used to improve the limited information about inverter parameters and operating state during renewable planning, which helps mitigate the uncertainty inherent in their integration.
Microbiology of Activated Sludge Bulking

Publisher Summary There are four main groups of filamentous microorganisms, which may cause bulking of activated sludge, namely, filamentous bacteria, actinomycetes, filamentous blue-green algae, and fungi. Nonfilamentous bulking is a high F/M ratio phenomenon and if the F/M ratio becomes high enough, the sludge deflocculates. The F/M ratio at which the sludge deflocculates depends upon the dissolved oxygen concentration in the mixed liquor and the level of turbulence in the aeration tank. The cure for nonfilamentous bulking is chlorination of the return sludge, which changes the surface properties of the floc particles and allows them to compact better, followed by building up the mixed liquor suspended solids (MLSS) so that the F/M ratio is reduced. Filamentous bulking is most frequently observed to occur in activated sludge systems with very low F/M ratios. The engineer's approach to solving a bulking problem is to skip the microscopic part and try to correlate the sludge volume index (SVI) with some operational parameter, such as F/M ratio or oxygen supply, or some waste water characteristics, such as the presence of carbohydrates, H 2 S, pH, or low nitrogen content.
Evaluation of Implementation of Coordinated School Health Policies in Lamar Consolidated Independent School District

Coordinated School Health is a model in which eight components of student health and wellness are weaved together in the school to help the student learn to live a healthier life. The purpose of this project was to evaluate how well the physical education and health education components of Coordinated School Health (CSH) were implemented in Lamar Consolidated Independent School District. A survey of 82 stakeholders was used to measure how well each campus has implemented the physical education and health education components of the CSH model. The information collected showed strengths and weaknesses in the CSH implementation at a district and campus level. Results indicated that both health education and physical education were well implemented within the district, with physical education lagging slightly behind health education. Suggestions for improvements at campus and district level are discussed in the last section of the paper.
Who Transitions from Private to Public Health Insurance?: Lessons from Expansions of the State Children's Health Insurance Program

This paper examines families of children who transition from private to public health insurance. These transitions include, but are not limited to, transitions that con- stitute crowd-out. We pool longitudinal panels from the Survey of Income and Program Participation (SIPP) covering 1990 to 2005. The annual rate of children who transition from private to public coverage more than doubled over this period, although it remains small. Transitioning children in recent years are typically in working families with median incomes of around 200% of poverty. Children who transition from private to public coverage are more likely to belong to minority groups, to have lower incomes, and to be in poorer health than children remaining privately insured. Public coverage now provides important protections for low-income working families, especially those with children in poor health. These findings underscore the need to implement post-health-reform policies with an eye towards possible adverse selection into public programs. common element of several recent insurance policy initiatives in the U.S. has been the establishment of public programs that provide coverage to the unin- sured alongside the continued offering of private health insurance. The passage of the State Children's Health Insurance Program (SCHIP), for example, led to an expansion of public health insurance provision to children above 200% of the poverty line. The recently enacted Patient Protection and Affordable Care Act (PPACA) further expanded Medicaid eligibility to adults with incomes below 133% of poverty. These program expansions and others have further embedded public coverage programs within our mixed private-public health care system. Under this mixed system, questions of crowd-out loom large. Crowd-out refers to the extent to which expansions of public coverage displace private insurance. 1 For
The Assembly of a Structural Lipoprotein in the Envelope of Escherichia coli

Abstract A major envelope protein of Escherichia coli was found to exist in two different forms in the envelope. One-third of the protein is covalently linked to the peptidoglycan (bound form) as found by Braun and his co-workers. The remaining two-thirds of the protein are in the envelope but are not covalently linked to the peptidoglycan (free form). In contrast to the free form, the bound form can only be solubilized by 1% sodium dodecyl sulfate (SDS) after lysozyme treatment of the envelope. The bound form thus solubilized shows a slightly higher molecular weight than the free form on SDS acrylamide gel electrophoresis because it has an attached peptidoglycan fragment. When E. coli cells were pulse-labeled with [3H]- or [14C]arginine for 4 min, all of the radioactivity of the protein in the envelope was found in the free form. Chasing with non-radioactive arginine showed that a portion of the free form was converted into the bound form. The ratio of the radioactivity in the free form to that in the bound form reached a constant level after chasing for one doubling time. These results indicate that the free form of the protein is first synthesized and then converted into the bound form. It appears that the reaction between the two forms is reversible and that there is a dynamic equilibrium between the two forms of the protein in the envelope. The conversion from the free form to the bound form was not inhibited by chloramphenicol, amino acid starvation (arginine), or carbonyl cyanide m-chlorophenylhydrazone.
JOINTLESS is a MADS-box gene controlling tomato flower abscission zone development

Abscission is a universal and dynamic process in plants whereby organs such as leaves, flowers and fruit are shed, both during normal development, and in response to tissue damage and stress. Shedding occurs by separation of cells in anatomically distinct regions of the plant, called abscission zones (AZs). During abscission, the plant hormone ethylene stimulates cells to produce enzymes that degrade the middle lamella between cells in the AZ. The physiology and regulation of abscission at fully developed AZs is well known, but the molecular biology underlying their development is not. Here we report the first isolation of a gene directly involved in the development of a functional plant AZ. Tomato plants with the jointless mutation fail to develop AZs on their pedicels and so abscission of flowers or fruit does not occur normally. We identify JOINTLESS as a new MADS-box gene in a distinct phylogenetic clade separate from those functioning in floral organs. We propose that a deletion in JOINTLESS accounts for the failure of activation of pedicel AZ development in jointless tomato plants.
Tetany and Chronic Diarrhea

Excerpt The infrequency of tetany as an accompaniment of diarrhea is attested by the fact that most contemporary writers on tetany rarely discuss diarrhea as an etiologic factor. The subject is bar...
Semanticorganizer: a customizable semantic repository for distributed NASA project teams

Semantic Organizer is a collaborative knowledge management system designed to support distributed NASA projects, including multidisciplinary teams of scientists, engineers, and accident investigators. The system provides a customizable, semantically structured information repository that stores work products relevant to multiple projects of differing types. Semantic Organizer is one of the earliest and largest semantic web applications deployed at NASA to date, and has been used in varying contexts ranging from the investigation of Space Shuttle Columbia's accident to the search for life on other planets. Although the underlying repository employs a single unified ontology, access control and ontology customization mechanisms make the repository contents appear different for each project team. This paper describes Semantic Organizer, its customization facilities, and a sampling of its applications. The paper also summarizes some key lessons learned from building and fielding a successful semantic web application across a wide-ranging set of domains with disparate users.
Designing a financial literacy course for a liberal arts curriculum

The broad objectives of liberal education include the instilling of a sense of responsible citizenship along with knowledge that creates a better society. Although financial literacy is required at both the individual and public levels for an improved societal outcome to ensue, it is rare to find a finance-related course within the general education curriculum of most universities. Liberal arts administrators and faculty are reluctant to include finance-related courses because they are not perceived to be sufficiently broad in scope. The argument is accurate for a typical personal finance course. However, the purpose of this article is to show that it is possible to construct a financial literacy course with design features that make it acceptable for inclusion in the general education curriculum of a liberal arts university. First, the objectives of liberal education are highlighted, as enumerated by three independent organizations [American Academy for Liberal Education (AALE), Association of American Colleges and Universities and the Annapolis Group]. Next, the assessment standards of the AALE are utilized to develop the pedagogical features of the course design. A liberal arts focus can be achieved by including topical readings, in-class discussions or debates and a research paper that highlights the societal impacts of financial decisions. Finally, it is illustrated how the design features allow the course to fulfil the assessment standards of liberal arts objectives including effective reasoning, broad and deep learning and the inclination to inquire.
The postsocialist transitions in comparative perspective: Policy issues and recent experience

Abstract This paper examines the postsocialist transition in Eastern Europe, the reforms in China and the “postdirigiste” transitions in Latin America. The paper analyzes: the initial conditions that gave rise to processes of reform in the different countries; the main strategies for economic reform—shock treatment, gradualism and mixed strategies—discussing their conditioning factors and rationale; the actual record of these policies in terms of key indicators of economic performance such as inflation, GDP growth, external sector sustainability, progress in privatization and the social costs of adjustment. In addition, the paper discusses interdependencies between economic and political reforms during the course of systemic transformation.
Local Lunar Topography from the Apollo 17 Alse Radar Imagery and Altimetry

The Apollo 17 ALSE (Apollo Lunar Sounder Experiment) VHF radar provided imagery and continuous profiling data around the moon during two revolutions. The imagery data are used to derive depth and diameter measurements of small craters (diameters less than 30 km). The profiling data are used to study the topography of a few large craters: the bulged floors in Hevelius, Neper, and Aitken; central peaks in Neper and Buisson; and the depressed floor of Maraldi. The same data provided accurate (better than 25 m) profiles of Mare Crisium and Mare Serenitatis.
Electron temperature in the solar wind at 1 AU

Knowing the total electron temperature of the solar wind is essential when calculating parameters that characterize it (for example, plasma beta and Mach number). Unfortunately, electron temperatures are not always available, and an educated guess must be made. A good rule of thumb is to assume that, at 1 AU, the total electron temperature of the ambient solar wind is a constant value of ∼140,000 K.
Prevalence and titer of IgE antibodies to mouse allergens.

Background Positive skin tests to allergens derived from mouse urine have been reported among patients with asthma. Very few data are available detailing the titer of IgE Ab to mouse allergen and how it varies by location and population. Objective To evaluate further the prevalence and titer of IgE Ab to mouse-derived allergens and their relevance to total IgE and asthma. Methods IgE Ab to mouse allergens was measured in 1165 sera from diverse populations including children and adults. The results were compared with IgE Ab to other allergens and total serum IgE. Results Positive results were found in 79 sera, but only 15 had an IgE Ab titer ≥10 IU/mL. Results for IgE Ab to Mus m 1 showed a close quantitative correlation with IgE Ab to mouse allergen ( r = 0.93; P Conclusion Mouse allergen sensitization may contribute significantly to total IgE and allergy in African American and Hispanic populations from some northern cities. Analysis of the significance of an IgE Ab response should include quantitative comparison with other responses and total IgE. Clinical implications Significance of rodent infestation and IgE Ab varies dramatically in different populations and areas of the United States.
Wavelet transform-based methods for denoising of Coulter counter signals

A process based on discrete wavelet transforms is developed for denoising and baseline correction of measured signals from Coulter counters. Given signals from a particular Coulter counting experiment, which detect passage of particles through a fluid-filled microchannel, the process uses a cross-validation procedure to pick appropriate parameters for signal denoising; these parameters include the choice of the particular wavelet, the number of levels of decomposition, the threshold value and the threshold strategy. The process is demonstrated on simulated and experimental single channel data obtained from a particular multi-channel Coulter counter processing. For these example experimental signals from 20 µm polymethacrylate and Cottonwood/Eastern Deltoid pollen particles and the simulated signals, denoising is aimed at removing Gaussian white noise, 60 Hz power line interference and low frequency baseline drift. The process can be easily adapted for other Coulter counters and other sources of noise. Overall, wavelets are presented as a tool to aid in accurate detection of particles in Coulter counters.
Evolutionary and structural feedback on selection of sequences for comparative analysis of proteins

It has been noted that slowly evolving protein residues have two properties: (a) they tend to cluster in the native fold, and (b) they delineate functional surfaces—parts of the surface through which the protein interacts with other proteins or small ligands. Herein, we demonstrate that the two are coupled sufficiently strongly that one effect, when observed, statistically implies the other. Detection of both can be accomplished in multiple sequence alignment related methods by the careful selection of relevant sequences. For the demonstration, we use two sets of protein families: a small set of diverse proteins with diverse functional surfaces, and a large set of homodimerizing enzymes. A practical outcome of our considerations is a simple prescriptive rule for the selection of homologous sequences for the comparative analysis of proteins: in order to optimize the detection of (potentially unknown) functional surfaces, it is sufficient to select sequences in such a way that the residues observed at any level of evolutionary divergence, as implied by the alignment, cluster on the folded protein. Proteins 2006. © 2006 Wiley-Liss, Inc.
MLPA: A Rapid, Reliable, and Sensitive Method for Detection and Analysis of Abnormalities of 22q

In this study, essential test characteristics of the recently described multiplex ligation-dependent probe amplification (MLPA) method are presented, using chromosome 22 as a model. This novel method allows the relative quantification of approximately 40-45 different target DNA sequences in a single reaction. For the purpose of this study, MLPA was performed in a blinded manner on a training set containing over 50 samples, including typical 22q11.2 deletions, various atypical deletions, duplications (trisomy and tetrasomy), and unbalanced translocations. All samples in the training set have been previously characterized by fluorescence in situ hybridization (FISH) with cosmid or BAC clones and/or cytogenetic studies. MLPA findings were consistent with cytogenetic and FISH studies, no rearrangement went undetected and repeated tests gave consistent results. At a relative change in comparative signal strength of 30% or more, sensitivity and specificity values were 0.95 and 0.99, respectively. Given that MLPA is likely to be used as an initial screening method, a higher sensitivity, at the cost of a lower specificity, was deemed more appropriate. A receiver operator characteristic (ROC) curve analysis was performed to calculate the most optimal threshold range, with associated sensitivity and specificity values of 0.99 and 0.97, respectively. Finally, performance of each individual probe was analyzed, providing further useful information for the interpretation of MLPA results. In conclusion, MLPA has proven to be a highly sensitive and accurate tool for detecting copy number changes in the 22q11.2 region, making it a fast and economic alternative to currently used methods. The current study provides valuable and detailed information on the characteristics of this novel method.
A custom-designed limited-angle actuator for an electromechanical engine valve drive part II: Fabrication and evaluation

Research has shown that variable valve timing (WT) can improve significantly the performance of internal combustion (IC) engines, including higher fuel efficiencies, lower emissions, and larger torque outputs at each point of the engine map. To achieve independent and continuous WT for each valve, an electromechanical valve drive (EMV) system with a custom-designed limited-angle actuator was proposed previously, whose feasibility with lower power consumption, smaller package, and faster transition was predicted by simulation. In order to validate the concept experimentally, a prototype actuator was built and evaluated in this paper. The fabrication considerations and assembling process of the prototype actuator are discussed before satisfactory experimental results of the whole EMV system with the prototype actuator are presented. A further projection for a full engine valve actuation illustrates a promising future of the EMV system with the limited-angle actuator in a real engine environment up to an engine speed of 6000 rpm. (6 pages)
Kinetics and mechanism of NH3 oxidation

The kinetics of NH 3 oxidation at 1279 to 1323 K have been studied experimentally witha flow tube reactor and theoretically by computer modelling. It was observed that the rate of NH 3 oxidation was zero order in NH 3 , increased with increasing [O 2 ], was inhibited by the presence of initial water, and promoted by the addition of H 2 or NO. During NH 3 oxidation, [NO] increased rapidly initially and more slowly thereafter. The size of the initial rise was independent of the presence or absence of H 2 O, while the subsequent increase was reduced by H 2 O. These and other kinetic features including the rate of oxidation of a trace of CO (a monitor of [OH]) are all quantitatively explained by a computer model. The major features of this model are conversion of NH 3 to NH 2 via reaction with O and OH, the reaction of NH 2 with O 2 , O, and OH to ultimately form NO, and the concurrent reduction of NO by NH 2 to ultimately yield N 2 . The chain carrier concentration during the process is regulated by a balance between carrier formation via the chain branching reactions and their removal by reactions such as NH 2 +HNO→NH 3 +NO.
Synthesis of N-acetylglucosamine thiazoline/lipid II hybrids

Abstract Potential inhibitors of transglycosylases involved in bacterial cell wall biosynthesis were synthesized by combining N -acetylglucosamine thiazoline, a potent inhibitor of β-hexosaminidase, with functional groups present in lipid II, the natural substrate of the transglycosylases.
A stochastic constitutive model for disordered cellular materials: Finite-strain uni-axial compression

Abstract A stochastic constitutive model is developed for describing the continuum-scale mechanical response of disordered cellular materials. In the present work, attention is restricted to finite-strain uni-axial compression under quasi-static loading conditions. The development begins with an established cellular-scale mechanical model, but departs from traditional modeling approaches by generalizing the cellular-scale model to accommodate finite strain. The continuum-scale model is obtained by averaging the cellular-scale mechanical response over an ensemble of foam cells. Various stochastic material representations are considered through the use of probability density functions for the relevant material parameters, and the effects of the various representations on the continuum-scale response are investigated. Combining cellular-scale mechanics with a stochastic material representation to derive a continuum-scale constitutive model offers a promising new approach for simulating the finite-strain response of cellular materials. Results demonstrate that increasing a material’s degree of polydispersity can produce the same stiffening effects as increasing the initial solid-volume fraction. Additionally, particular stochastic material representations are shown to provide upper and lower bounds on the mechanical response of the cellular materials under investigation, while suitable choices for the stochastic representation are shown to accurately reproduce experimental stress–strain data through the large deformations associated with densification.
Seeing landscape: geography, autobiography, and metaphor

Writing about the value and significance of landscape, Denis Cosgrove has argued that ‘[l]andscape is a way of seeing the world’.1 While I agree with this definition of landscape as a means of inte...
Electron density fluctuations in the local interstellar bubble

The interstellar medium in our vicinity forms an elongated cavity of X-ray-emitting gas, extending up to 200 pc from the Sun. The gas inside this local bubble is very hot (~ 10^6 K) and tenuous (electron density n _e ≈ 0.005 cm^(−3)), and is typical of material in the coronal phase of the interstellar medium, thought to occur when hot stars or supernovae blow out holes in cooler and denser interstellar gas. Little is known about turbulent density fluctuations in the coronal gas, but its physical state is important in understanding cosmic ray confinement and the energy balance of interstellar material, as well as the scattering of radio emission from compact sources. To probe turbulence in the local interstellar medium, we have made scintillation measurements at 50 MHz (6 m wavelength) of emission from the nearby pulsar 0950 + 08, which happens to lie near the edge of the local bubble. From the scintillation bandwidth we deduce the amplitude of the electron-density fluctuation spectrum in the coronal gas alone, and find it to be an order of magnitude lower than for any previously measured interstellar line of sight. We conclude that the interior of the bubble is relatively quiescent and that high levels of plasma turbulence—if they exist—must be localized to the cavity boundary.
Isothermal crystallization of poly(vinylidene fluoride) in the presence of high static electric fields. I. Primary nucleation phenomenon

Primary nucleation of poly(vinylidene fluoride) (PVF2) γ-phase crystals from the melt is affected by the presence of an electric field. Crystallization under the electric field is studied by polarized optical microscopy, thermal analysis, and wide-angle x-ray diffraction. Preliminary results indicate that the γ-phase crystal nucleation rate and content are enhanced by the electric field. A modification of the classical theory of homogeneous nucleation of a crystalline phase is proposed to account for the experimental observations. Electrostatic interaction between the nucleus total polarization and the electric field contributes to the free energy of nucleation to a very large extent at low undercooling. Theoretical predictions indicate that a static electric field will increase the nucleation rate of a polar phase and will decrease the nucleation rate of a nonpolar phase. Confirmation of the former fact is observed experimentally.
A prospective evaluation of dietary status and symptoms after near-total esophagectomy without gastric emptying procedure

Abstract Background: After esophagectomy, the stomach is the most commonly utilized reconstructive conduit. There remains debate among surgeons regarding the requirements for pyloroplasty/pyloromyotomy following reconstruction. We present a series of patients having undergone near total esophagectomy and reconstruction with gastric tube without gastric emptying procedure to analyze critically these patients’ ability to reestablish a subjectively acceptable and nutritionally adequate eating pattern without significant side effects of early satiety, dumping, or diarrhea. Methods: Between 1991 and 1998, 48 patients underwent esophagectomy utilizing this technique and were available for long-term follow-up and nutritional assessment. Patient weights were recorded at 2 weeks, 6 months, and 1 year and a telephone interview conducted at a mean of 36 months postoperatively for the evaluation of eating patterns and symptoms. A subgroup of these patients (32 of 48) completed a 3-day dietary record that was assessed by a certified nutritionist. This patient group included 10 patients (21%) who had received perioperative chemoradiotherapy. Results: Dietary intake was characterized as normal or minimally limited in 41 patients (85%). Those who had received perioperative chemoradiotherapy needed no significant increased time to return to a normal dietary baseline (6.1 versus 5.9 months). Mean weight loss prior to surgery was 3 kg. Weight loss continued for the first 6 months (mean 10 kg); however, 63% were able to gain weight from 6 months to 1 year following surgery (mean 3 kg). Most patients were overweight prior to operation (mean 115% of ideal body weight) and achieved a new postoperative baseline (mean 104% of ideal body weight) at 1 year. Patients demonstrated a mean daily caloric intake of 2,179 kilocalories per day, which was 98% of recommended according to their ideal body weight. Postoperative symptoms of short-term nausea (19%), occasional dysphagia with certain foods (38%), mild increased stool frequency (15%), and occasional regurgitation (25%) were noted. Conclusions: Near-total esophagectomy with verticalized gastric tube without a gastric emptying procedure is well tolerated and allows a return to subjectively acceptable and nutritionally appropriate dietary eating pattern without significant associated side effects.
Locking and robustness in the finite element method for circular arch problem

In this paper we discuss locking and robustness of the finite element method for a model circular arch problem. It is shown that in the primal variable (i.e., the standard displacement formulation), the p-version is free from locking and uniformly robust with order\(p^{-k}\) and hence exhibits optimal rate of convergence. On the other hand, the h-version shows locking of order \(h^{-2}\), and is uniformly robust with order \(h^{p-2}\) for \(p>2\) which explains the fact that the quadratic element for some circular arch problems suffers from locking for thin arches in computational experience. If mixed method is used, both the h-version and the p-version are free from locking. Furthermore, the mixed method even converges uniformly with an optimal rate for the stress.
Abstract 3619: The absence of cleaved caspase-3 in circulating tumor cells detected using a non-enrichment-based assay

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Background: The role of cleaved caspase-3 as an integral player in the apoptotic process of mammalian cells has prompted the investigation of an assay to detect cleaved caspase-3 in circulating tumor cells (CTCs) as one way to assess CTC viability. Methods: Using a previously developed non-enrichment based assay, nucleated blood cells and CTCs are adhered to a single slide. An antibody for cleaved caspase-3 was incorporated into the assay in addition to the existing antibodies for cytokeratin (to identify tumor cells) and CD45 (to identify white blood cells), as well as a nuclear stain (DAPI). The modified assay was initially tested on cultured MCF 10a cells spiked into normal donor blood. Before spiking, apoptosis was induced in these cells using staurosporine. Following validation of the assay in cell lines, the assay was performed using blood samples from 9 different breast cancer patients, as well as 3 different normal donor samples. Results: CTCs were detected in the patient samples as single cells, as well as clusters. The results of the assay showed that only 1 out of 896 detected CTCs was positive for cleaved caspase-3 (0.11%). Of these CTCs, 134 of them were found to be in clusters, and all 134 were negative for cleaved caspase-3, indicating that whether in clusters or as single cells, the vast majority of CTC's detected with this assay are not undergoing irreversible apoptotic processes via cleaved caspase-3. The results also showed that 0.40% of white blood cells in healthy donors expressed cleaved caspase-3, compared to 0.51% of the white cells in cancer patients, indicating that healthy donors and cancer patients express cleaved caspase-3 in their white blood cells at nearly the same rate. Conclusions: The morphologic characterization used in this platform to select healthy-appearing cells identifies a population of circulating tumor cells with virtually no evidence of caspase-related ongoing apoptosis, a finding that supports the morphologic impression of viability. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3619. doi:1538-7445.AM2012-3619