cssi/SciSciGPT-SciSciNet huggingface dataset:
A supervised clustering method for text classification

This paper describes a supervised three-tier clustering method for classifying students' essays of qualitative physics in the Why2-Atlas tutoring system. Our main purpose of categorizing text in our tutoring system is to map the students' essay statements into principles and misconceptions of physics. A simple ‘bag-of-words' representation using a naive-bayes algorithm to categorize text was unsatisfactory for our purposes of analyses as it exhibited many misclassifications because of the relatedness of the concepts themselves and its inability to handle misconceptions. Hence, we investigate the performance of the k-nearest neighborhood algorithm coupled with clusters of physics concepts on classifying students' essays. We use a three-tier tagging schemata (cluster, sub-cluster and class) for each document and found that this kind of supervised hierarchical clustering leads to a better understanding of the student's essay.
Student Perceptions of Web-Assisted Teaching Strategies.

This study determines which Web-assisted teaching strategies social work students from a single university experience and perceive as valuable. The results demonstrate that most faculty use email, post grades online, and give out student email addresses to the class. Students perceive email communication with the instructor and the online provision of course information as the most valuable strategies. The impact of several student characteristics on value perception is also examined, revealing varying levels of influence. These findings suggest that the strategies students report as the most valuable are not necessarily the strategies most frequently used by faculty.
Treatment of hypertension in patients with renal artery stenosis due to fibromuscular dysplasia of the renal arteries

Renal artery stenosis (RAS) from fibromuscular dysplasia (FMD) is an uncommon cause of hypertension that affects mostly women. FMD is a noninflammatory vascular disease that predominantly affects mainly the renal arteries, but can also affect arteries in other vascular territories. The most common type of FMD is the media fibroplasia with the characteristic “string of beads” appearance (80-90%), whereas the two other types, the “intimal” and “adventitial” FMD are much less common accounting for 10% and <5% of cases, respectively. The prevalence of FMD in the general population is not well known. Estimates are derived from screening kidney donors, with a prevalence of about 2.6%. Among patients with renovascular hypertension (RVH), its incidence is about 10%, whereas 80-90% of RVH is due to atherosclerotic renal artery stenosis (ARAS). The treatment of choice of hypertension due to FMD is percutaneous renal angioplasty (PTRA). In contrast, hypertension due to ARAS is not frequently responsive to PTRA. In order to achieve successful control of hypertension in patients with FMD, a combination of PTRA with drugs that block the renin-angiotensin-aldosterone system (RAAS) is often necessary. The purpose of this review was to search the literature for newer diagnostic methods and treatment of FMD. Therefore, a Medline search of the English literature of published papers between 2008 and December 2013 was performed. Of 58 papers reviewed, 19 pertinent papers were selected including, studies, reviews, registries and case reports. The information from these studies together with collateral literature will be discussed in this concise review.
Serum prostate-specific antigen decline as a marker of clinical outcome in hormone-refractory prostate cancer patients: association with progression-free survival, pain end points, and survival.

PURPOSE: Validated end points are lacking for clinical trials in hormone-refractory prostate cancer (HRPC). Controversy remains regarding the utility of a posttreatment decline of prostate-specific antigen (PSA). The purpose of this study was to determine whether posttreatment declines in PSA were associated with clinical measures of improvement in a randomized phase III trial of suramin plus hydrocortisone versus placebo plus hydrocortisone. PATIENTS AND METHODS: A total of 460 HRPC patients were randomized to receive suramin plus hydrocortisone (n = 229) or placebo plus hydrocortisone (n = 231). All patients had symptomatic, metastatic HRPC requiring opioid analgesics. Clinical end points evaluated included overall survival, objective progression-free survival (OPFS), and time to pain progression (TTPP). An evaluation of overall survival, OPFS, and TTPP as a function of a PSA decline of ≥ 50%, lasting at least 28 days, was undertaken by using a landmark analysis at 6, 9, and 12 weeks. A multivariate ana...
Internationalizing the Business Curriculum: A South Korean Case Study.

Accrediting agencies for Colleges and Schools of Business such as the Association to Advance Collegiate Schools of Business International (AACSB) and the Association of Collegiate Business Schools and Programs (ACBSP) require that business programs incorporate both an international dimension and an active learning component in developing their business curriculum. One avenue business schools can use to accomplish both of these goals is to provide abbreviated study abroad programs for students and faculty. Rather than spending an entire semester abroad (which many smaller schools cannot afford to do financially), one approach is to take 10 – 15 students and spend 7 – 10 days in a country. This paper presents one case study using this approach - An 8 day Study Abroad Trip to South Korea - and discusses the following areas: logistics, pre-trip preparation, trip activities, and post-trip activities. While this case study focuses on South Korea, it provides a model for international study abroad that helps business schools meet accreditation standards and internationalize their curriculum.
Transient proton uptake and release is associated with the photocycle of the photoactive yellow protein from the purple phototrophic bacterium Ectothiorhodospira halophila

Abstract Upon excitation by a laser flash at 445 nm, the photoactive yellow protein (PYP) undergoes a bleach and red-shift occurring in less than 10 ns, undergoes a further bleach in ≈200 μs, and then recolors in ≈200 ms. A conformational change occurs during photobleaching which exposes a hydrophobic site. We have now shown that this photocycle also involves a net uptake of one proton during formation of the fully bleached second intermediate, followed by an equivalent proton release upon return of PYP to the ground state. Proton uptake lags slightly behind PYP bleaching and is first-order, indicating that the protein conformational change occurs in two steps. The results suggest that a basic residue which is normally buried in the protein interior is transiently exposed to solvent during the PYP photocycle and, as a consequence, undergoes a change in pK. On the basis of the crystal structure of PYP, we propose that this basic residue is lysine 111.
Cooperative Interaction and Intergroup Bias: Effects of Numerical Representation and Cross-Cut Role Assignment

This study investigates whether the greater in-group favoritism typically expressed by numerical minorities could be minimized by cross-cutting role assignment to the tasks in a cooperative setting. Study 1 manipulated the numerical representation of two groups and role assignment to a team task. The results showed that cross-cut role assignment decreased the in-group bias of both minority and majority groups, compared to convergent role assignment. Study 2 further examined the benefits of cross-cut assignment while controlling interaction among in-group and out-group members. The outcomes of Study 2 replicated those of Study 1 and showed that even without prior interaction during the cross-cut task, both minorities and majorities were less biased when role assignments cross-cut category membership. Moreover, the results showed that whereas both social category salience and identification were affected by role assignment, only identification mediated the effect of role assignment on in-group bias.
Abstract C113: p21 downregulation is an important component of PAX3/FKHR oncogenicity and its reactivation by histone deacetylase inhibitors enhances combination treatment

A number of drugs developed against cancer‐specific molecular targets have been shown to offer survival benefits alone or in combination with standard treatments, especially for those cases where tumor pathogenesis is dominated by a single molecular abnormality. One example for such a tumor type is alveolar rhabdomyosarcoma (aRMS) which is characterized by a specific translocation creating the oncogenic PAX3/FKHR transcription factor, believed to be the main molecular basis of the disease. Recently, we were able to demonstrate that the small molecule inhibitor PKC412 exhibits strong antitumor activity against aRMS by reducing the transcriptional activity of PAX3/FKHR. In the present study, we screened for combination strategies that are superior to PKC412 treatment alone. Interestingly, we found that the combination of PKC412 with histone deacetylase (HDAC) inhibitors like valproic acid (VPA) synergistically induced apoptosis resulting in suppressed aRMS tumor growth in vivo. We provide evidence that the enhanced antitumor effect upon combination treatment is achieved by VPA‐induced reactivation of p21 which is downregulated in aRMS tumor cells via destabilization of its transcriptional regulator EGR1 by PAX3/FKHR. This identifies downregulation of p21 as a crucial event in PAX3/FKHR oncogenicity. Our study not only highlights a possible mechanism behind the increased efficacy of combination treatment but also indicates that different levels of PAX3/FKHR oncogenicity can be exploited therapeutically by a specific combination of anticancer drugs to increase their therapeutic potential. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):C113.
Effects of diazinon on macroinvertebrates and insect emergence in outdoor experimental channels

Abstract Effects of diazinon on macroinvertebrates were assessed in three outdoor experimental channels from mid-May to mid-September, 1980. One channel served as a control and two channels as low and high treatments. Three dosing regimes were employed. The low and high treatment channels were continuously dosed for 12 wk to nominal concentrations of 0.3 and 3 μg/l, then increased to 6 and 12 μg/l for 4 wk, then the high treatment was increased to 30 μg/l with the low treatment channel returned to ambient. Diazinon concentrations did not reach the intended levels during the latter two dosing regimes. No consistent interchannel differences were observed in total macroinvertebrate abundance or in species diversity induces. Effects were noted at the lowest concentration for amphipods and insects. As diazinon concentrations were increased interchannel community structure changes became more pronounced. Elevated drift, especially amphipods and snails, occurred in the treated channels 4 wk after dosing began and following the increases in concentrations. Total numbers and species of insects emerging from the three channels were not greatly different but lower numbers of mayflies and damselflies emerged from the treated channels. Tolerance of macroinvertebrates to diazinon were as follows: flatworms, physid snails, isopods and chironomids most tolerant; leeches and the amphipod Crangonyx less tolerant; the amphipod Hyalella, mayflies, caddisflies and damselflies sensitive.
Linearization of data for saturation-type competitive protein binding assay and radioimmunoassay

Most of the commonly-performed competitive protein-binding radioassay methods utilized in the clinical laboratory are based on the principle of saturation analysis. Although many different methods for linearization of saturation-type assays have been proposed, the algebraic equivalency of all of these methods has not been adequately documented. In this manuscript we have shown the physical and mathematical basis for various methods for linearlization of saturation type assays and the algebraic equivalency of these linearization methods. We have also shown that key parameters such as slope and intercept may be dependent on different components of the assays system with differnt linearization methods. An understanding of these key parameters can help the analyst to evaluate changes in these key parameters and to integrate these parameters in a complete quality control system.
Wave-function shock waves

When a Rydberg state is suddenly excited to an autoionizing Rydberg state by a short-pulse core-electron excitation, a shock wave is created in the Rydberg electron's wave function. This shock wave originates at small r, at the excited core, and propagates outward. This wave-function disturbance is best illustrated by the Rydberg wave function in momentum space, where the autoionization process can be seen as a filtering process that reduces the high-momentum, outgoing wave function.
Literature on pederasty

Abstract As an aspect of research into pederasty, the author suggests that deeper insights into feelings and emotions, and aspects not usually discussed in scientific articles, might be obtained from an examination of biographies and biographical novels, from specifically pederast novels as well as from fiction with pederast incidents. The volume of legal, historical, fictional and psychological material shows that there is much more sexual involvement between men and boys than has been commonly believed.
Brain-penetrant LSD1 inhibitors can block memory consolidation

Modulation of histone modifications in the brain may represent a new mechanism for brain disorder therapy. Post-translational modifications of histones regulate gene expression, affecting major cellular processes such as proliferation, differentiation, and function. An important enzyme involved in one of these histone modifications is lysine specific demethylase 1 (LSD1). This enzyme is flavin-dependent and exhibits homology to amine oxidases. Parnate (2-phenylcyclopropylamine (2-PCPA); tranylcypromine) is a potent inhibitor of monoamine oxidases and derivatives of 2-PCPA have been used for development of selective LSD1 inhibitors based on the ability to form covalent adducts with flavin adenine dinucleotide (FAD). Here we report the synthesis and in vitro characterization of LSD1 inhibitors that bond covalently to FAD. The two most potent and selective inhibitors were used to demonstrate brain penetration when administered systemically to rodents. First, radiosynthesis of a positron-emitting analog was used to obtain preliminary bio-distribution data and whole brain time-activity curves. Second, we demonstrate that this series of LSD1 inhibitors is capable of producing a cognitive effect in a mouse model. By using a memory formation paradigm, novel object recognition, we show that LSD1 inhibition can abolish long-term memory formation without affecting short-term memory, providing further evidence for the importance of reversible histone methylation in the function of the nervous system.
Plasma lipid levels and colorectal adenoma risk

Purpose Abnormalities in lipid levels have been associated with colorectal neoplasm risk; however, few studies have adjusted for use of cholesterol-lowering medications. The objective of this study was to determine the association of plasma lipid levels with adenoma risk while accounting for statin medication use.
Elastic energy of curvature-driven bump formation on red blood cell membrane

Model calculations were performed to explore quantitative aspects of the discocyte-echinocyte shape transformation in red blood cells. The shape transformation was assumed to be driven by changes in the preferred curvature of the membrane bilayer and opposed by the elastic shear rigidity of the membrane skeleton. The energy required for echinocyte bump formation was calculated for a range of bump shapes for different preferred curvatures. Energy minima corresponding to nonzero bump heights were found when the stress-free area difference between the membrane leaflets or the spontaneous curvature of the membrane became sufficiently large, but the calculations predict that the membrane can tolerate significant differences in the resting areas of the inner and outer leaflets or significant spontaneous curvature without visible changes in shape. Thus, if the cell is near the threshold for bump formation, the calculations predict that small changes in membrane properties would produce large changes in cellular geometry. These results provide a rational framework for interpreting observations of shape transformations in red cells and for understanding the mechanism by which small changes in membrane elastic properties might lead to significant changes in geometry.
THE MEASUREMENT OF OXYGEN TRANSPORT PARAMETERS FOR ASPHALT/AGGREGATE AND ASPHALT/GLASS SYSTEMS USING AN ELECTRODYNAMIC BALANCE

ABSTRACT A gravimetric method using an eledrodynamic balance was developed for the measurement of transport properties such as the diffusion coefficient, D, solubility, S, and permeability, P, for oxygen into thin layers of asphalt materials deposited on aggregate and glass particles. Glass spheres and aggregate particles in the 14 to 50 μm size range coated with asphalt materials (AAB1, AAG1, and AAK1) were suspended contactless in the balance to measure D, S, and P in the temperature range 21 to 61° C. Transport parameters were determined from the changes in the particle mass due to the uptake of oxygen by the asphalt coating on glass spheres and nonspherical aggregate particles.
Fibroblasts Induce Mechanical Changes in the Extracellular Environment and Enhance Capillary-Like Network Formation

Cardiac tissue engineering studies have demonstrated the importance of revascularization in engineered grafts for successful implantation and regeneration [1]. Understanding the myocardium’s complex cellular organization and the interactions between the major cardiac cell types (cardiomyocytes, endothelial cells, and cardiac fibroblasts) is critical for revascularization. Our previous studies have shown the importance of cardiomyocyte-endothelial interactions [2]. However, there is limited information available on endothelial-fibroblast interactions. We and others have previously observed that during capillary assembly, fibroblasts provide chemical signaling via expression of growth factors [3, 4]. In addition, fibroblasts may also regulate angiogenesis through alterations to the mechanical environment via myocardial remodeling, including matrix degradation and deposition, and tissue contraction. Changes to the extracellular mechanical enviroment may lead to changes in basic cell functions such as proliferation, apoptosis, and growth factor expression.Copyright © 2008 by ASME
Postnatal dendritic development in the rabbit visual cortex.

Summary Golgi preparations of rabbit visual cortex aged 1–25 days, as well as similar tissues from adults, were examined for the growth of the dendritic arbor, and in particular the development of dendritic spines. The layer 5 pyramidal neurons and layer 4 stellate neuron were chosen as representatives of larger classes of neurons in the visual cortex. It was determined that the growth of the dendritic arbor, determined by counts of total number of dendritic and total dendritic length, is quite similar for pyramidal and stellate neurons. Dendritic spine development, however, is more rapid in pyramidal neurons than in stellate. This disparity in the rate of dendritic spine development is discussed in the light of physiologic studies on the development of receptive field properties in the rabbit visual cortex.
Elevation of fibronectin levels in lung secretions of infants with respiratory distress syndrome and development of bronchopulmonary dysplasia.

To determine whether the level of fibronectin in lung secretions correlates with the severity of lung injury or with the development of bronchopulmonary dysplasia, or both, serial tracheal aspirate samples were collected from 32 preterm infants with severe respiratory distress syndrome. Levels of total fibronectin, cellular fibronectin, plasma fibronectin, albumin, and secretory component of IgA (SC) were determined for the first 1 to 2 weeks of life in the 14 infants who recovered without pulmonary sequelae, and for weeks 1 to 4 in the 18 infants in whom bronchopulmonary dysplasia developed. Secretory component was chosen as the reference protein because its concentration in lung secretions is minimally influenced by capillary leak and does not vary with gestational or postnatal age. Albumin/SC and plasma fibronectin/SC ratios in tracheal aspirates were significantly higher ( p p
The management of neuromuscular ventilatory failure

All patients with respiratory impairment have either primarily ventilatory or primarily oxygenation impairment. Patients with neuromuscular conditions fall into the former category but are all too often managed as though they had the latter with oxygen therapy, bronchodilators, chest physical therapy, intermittent positive pressure breathing, and so on. This approach can only hasten respiratory failure and management by tracheostomy. However, it has been reported that with the use of noninvasive respiratory muscle aids, respiratory morbidity and mortality can be prevented for most patients with neuromuscular disease without resort to tracheostomy or even hospitalization.
Maternal patterns of postpartum alcohol consumption by age: a longitudinal analysis of adult urban mothers.

The purpose of this study is to investigate a) longitudinal patterns of maternal postpartum alcohol use as well as its variation by maternal age at child birth and b) within maternal age groups, the association between other maternal characteristics and alcohol use patterns for the purposes of informed prevention design. Study sample consists of 3397 mothers from the Fragile Families and Child Wellbeing Study representing medium and large US urban areas. Maternal drinking and binge drinking were measured at child age 1, 3, and 5 years. We conducted separate longitudinal latent class analysis within each of the three pre-determined maternal age groups (ages 20–25, n = 1717; ages 26–35, n = 1367; ages 36+, n = 313). Results revealed different class structures for maternal age groups. While two classes (NB [non-binge]-drinkers and LL [low-level]-drinkers) were identified for mothers in each age group, a third class (binge drinkers) was separately distinguished for the two older age groups. Whereas binge drinking rates appear to remain stable over the 5 years postdelivery for mothers who gave birth in their early twenties, mothers ages 26 and older increasingly engaged in binge drinking over time, surpassing the binge drinking behavior of younger mothers. Depression significantly increases the odds of being a NB-drinker for the 20–25 age group and that of being a binge drinker for the 36+ age group, whereas smoking during pregnancy is associated with subsequent binge drinking only for mothers ages 20–25. Findings highlight the importance of distinguishing risk factors by maternal age groups for drinking while parenting a young child, to inform the design of intervention strategies tailored to mothers of particular ages.
Catecholaminergic mechanisms of reinforcement: Direct assessment by drug self-administration

Abstract Reinforcing qualities in rats were shown by i.v. doses of two dopaminergic agonists, apomorphine and piribedil, and one noradrenergic agonist, clonidine, both in tests for primary reinforcement as seen in self-administration behavior and for conditioned reinforcement. Pretreatment with a dopaminergic blocker (haloperidol) interfered with the reinforcing effectiveness of apomorphine whereas an inhibitor of norepinephrine biosynthesis (U-14, 624) did not. Haloperidol also inhibited piribedil-based reinforcement. Pretreatment with an α-adrenergic blocking agent (phenoxybenzamine) inhibited the reinforcing effect of clonidine. These studies indicate that activation of either central dopaminergic or noradrenergic receptors can result in positive reinforcing effects.
365 ANALYSIS OF DRUG PRESCRIBING INFORMATION FOR PEDIA-TRICS AND OBSTETRICS AS PRESENTED IN THE PHYSICIANS DESK REFERENCE

In order to assess the impact of the recent upsurge in pediatric drug research, the 1980 edition of the Physicians Desk Reference was reviewed for data and indications pertaining to pediatric and obstetric usage. A total of 1.133 entries were reviewed. Of these 71.9% were oral preparations, 20% parenteral, 1.6% various other routes of administration and 6.5% included multiple routes. Dosing data based on weight or surface area was provided in 27.8% of entries. Specific pediatric dosing data was provided in 40.9% of entries while pediatric usage was specifically contraindicated in 8.9% of entries. In 39.1% of entries no mention was made of pediatric usage and in 11.1% it was mentioned, but without clear recommendations or data. In 2.6% of entries use in pregnancy was approved while 10.3% contained a definite contraindication for such use. The remaining entries either failed to mention use in pregnancy (31.8%) or mentioned use in pregnancy but without definite recommendation (55.3%). Use in breast feeding mothers was mentioned in 27.9% of entries with data provided in 107 entries and a definite contraindication in 104. Data on overdose management was provided in 29.8% of entries. Marked variability was noted between drug classes and manufacturers in terms of the information provided. It is clear from the above analysis that a continued emphasis is needed by manufacturers on providing solid data pertaining to drug usage in pediatrics and obstetrics.
MbtH-Like Proteins as Integral Components of Bacterial Nonribosomal Peptide Synthetases †

The biosynthesis of many natural products of clinical interest involves large, multidomain enzymes called nonribosomal peptide synthetases (NRPSs). In bacteria, many of the gene clusters coding for NRPSs also code for a member of the MbtH-like protein superfamily, which are small proteins of unknown function. Using MbtH-like proteins from three separate NRPS systems, we show that these proteins copurify with the NRPSs and influence amino acid activation. As a consequence, MbtH-like proteins are integral components of NRPSs.
Congenital Malformations of the Lung and Mediastinum-A Quarter Century of Experience From a Single Institution

Congenital malformations of the lung are rare and vary widely in their presentation and severity. The authors reviewed 25 years of experience with specific reference to diagnosis, treatment, and outcome. From July 1970 to June 1995, 70 patients were diagnosed with congenital malformations of the lung, which included sequestration (n = 20), foregut anomalies (n = 20), congenital lobar emphysema (CLE; n = 10), congenital cystic adenomatoid malformation (CCAM; n = 5), benign lung cysts (n = 6), lung aplasia/ hypoplasia (n = 4), and other miscellaneous disorders (n = 5). All patients with pulmonary hypoplasia presented at birth. With the exception of one patient, infants with CCAM and CLE presented before 5 months of age. All other patients presented from birth to 16 years of age. A prenatal diagnosis was accurate in two patients. Although prompt surgical management is the rule, the exceptions were children with bilateral lung involvement. Corrective surgery was delayed in some patients in whom extended respiratory support was required or in whom the delay led to an increase in pulmonary reserve. Extracorporeal membrane oxygenation (ECMO) was used in two patients pre- and postoperatively to manage persistent pulmonary hypertension. This review, representing the largest series of congenital lung lesions, showed that (1) prenatal diagnosis is useful but generally does not change the outcome; (2) computerized tomography (CT) is the optimum postnatal diagnostic imaging modality if chest radiography is not definitive; (3) ECMO can be an adjunct in treating associated pulmonary hypertension; (4) pulmonary resection (lobectomy) is the surgical procedure of choice for most lesions; (5) expected survival is good; and (6) pulmonary hypertension is the most common cause of mortality.
Role of microtubules in glucose uptake by C6 glioma cells

Drugs that influence tubulin function were used to investigate the role of microtubules in hexose uptake by C6 glioma cells. In C6 cells, colchicine and vinblastine (which inhibit tubulin polymerization) inhibited radioactive [3H]2-deoxy-D-glucose uptake by about 30%. Paclitaxel (which promotes tubulin polymerization) stimulated hexose uptake by about 25%. To further demonstrate that microtubules play a role in hexose uptake, C6 cells were transfected with GLUT1 cDNA and then challenged with 100 nM paclitaxel. In GLUT1-transfected cells paclitaxel stimulated 2-deoxy-D-glucose uptake by about 35%. To study the role of tubulin in agonist-stimulated hexose uptake, the effect of colchicine on carbachol-induced uptake was next examined. Hexose uptake was increased with carbachol in concentration-dependent manner which was abolished by pretreatment with colchicine. To examine the specificity of the inhibitory effect of colchicine on G protein-mediated signal transduction pathway, the influence of colchicine on insulin (which acts via tyrosine kinase pathway) stimulation of 2-deoxy-D-glucose uptake was investigated. Hexose uptake was increased by insulin in a concentration-dependent manner which was unaffected by pretreatment with colchicine. These results suggest that microtubules are involved in basal and carbachol-stimulated glucose uptake by C6 cells.
A 43-year-old woman with chest pressure.

She has acute chest discomfort, a 25-pack-year smoking history, and a family history of myocardial infarction and deep vein thrombosis. What is the cause of her symptoms?
Protein dynamics in the bacteriorhodopsin photocycle: submillisecond Fourier transform infrared spectra of the L, M, and N photointermediates

The usefulness of stroboscopic time-resolved Fourier transform IR spectroscopy for studying the dynamics of biological systems is demonstrated. By using this technique, we have obtained broadband IR absorbance difference spectra after photolysis of bacteriorhodospin with a time resolution of approximately 50 microseconds, spectral resolution of 4 cm-1, and a detection limit of delta A less than or equal to 10(-4). These capabilities permit observation of detailed structural changes in individual residues as bacteriorhodopsin passes through its L, M, and N intermediate states near physiological temperatures. When combined with band assignments based on isotope labeling and site-directed mutagenesis, the stroboscopic Fourier transform IR difference spectra show that on the time scale of the L intermediate, Asp-96 has an altered environment that may be accompanied by change in its protonation state. On the time scale of the L----M transition, this Asp-96 perturbation/deprotonation is largely reversed, and Asp-85 becomes protonated. During the M----N transition, Asp-85 appears to remain protonated but undergoes a change in its environment as evidenced by a shift of vC = O from 1761 to 1755 cm-1. The retention of a proton on Asp-85 in the N state indicates that the proton transferred from the Schiff base to this residue in the L----M step is not released to the extracellular medium during the same photocycle, but rather during a subsequent one. Also during the M----N transition, Asp-96 undergoes a deprotonation (possibly for the second time in a single photocycle). Bands in the amide I and amide II spectral regions in the M----N difference spectrum indicate the occurrence of a conformational change involving one or more peptide groups in the protein backbone.
THE NEW PHILOSOPHY OF CHEMISTRY AND ITS RELEVANCE TO CHEMICAL EDUCATION

This article tries to analyze briefly the reasons why philosophy of chemistry has only recently emerged, whereas the philosophical study of physics and biology are far better established fields of knowledge. Some key issues in contemporary philosophy of chemistry are reviewed and the ways in which this new branch of philosophy of science can be of potential benefit to chemical education are discussed. [Chem. Educ. Res. Pract. Eur.: 2001, 2, 165-170]
Karyotypic Variation within Clonal Lineages of the Rice Blast Fungus, Magnaporthe grisea

We have analyzed the karyotype of the rice blast fungus, Magnaporthe grisea, by using pulsed-filed gel electrophoresis. We tested whether the electrophoretic karyotype of an isolate was related to its pathotype, as determined by infection assays, or its genetic lineage, as determined by DNA fingerprinting. Highly reproducible electrophoretic karyotypes were obtained for a collection of U.S. and Chinese isolates representing a diverse collection of pathotypes and genetic lineages. Chromosomes ranged in size from 3 to 10 Mb. Although chromosome number was largely invariant, chromosome length polymorphisms were frequent. Minichromosomes were also found, although their presence was not ubiquitous. They ranged in number from 1 to 3 and in size from 470 kb to 2.2 Mb. Karyotypes were sufficiently variable as to obscure the obvious relatedness of isolates on the basis of pathogenicity assays or genetic lineage analysis by DNA fingerprinting. We documented that the electrophoretic karyotype of an isolate can change after prolonged serial transfer in culture and that this change did not alter the isolate's pathotype. The mechanisms bringing about karyotype variability involve deletions, translocations, and more complex rearrangements. We conclude that karyotypic variability in the rice blast fungus is a reflection of the lack of sexuality in wild populations which leads to the maintenance of neutral genomic rearrangements in clones of the fungus.
Irenaeus as Logos Theologian

Abstract Despite the prevalence of “Logos” as a christological title in his works, Irenaeus of Lyons has not been considered a Logos theologian due to an untenable presupposition that the Greek doctrine of the Logos has no place in the biblical thought of Irenaeus. The purpose of this article is to study Irenaeus’ use of “Logos” in explaining the nature and work of the Second Person, particularly in his pre-incarnational state. Furthermore, I read Irenaeus in conjunction with Justin’s Logos theology to demonstrate that Irenaeus alters the dominant understanding of Logos theology in the second century. In Irenaeus’ works, the title “Logos” functions to unite the Father and Son in one, equal divine nature, allowing the Son to work on behalf of the Father in creation as an agent of creation and revelation.
Immunocytochemical and biochemical characterization of glial phenotypes in normal and immortalized cultures derived from 3-day-old chick embryo encephalon.

We examined properties of glia derived from very early neurogenesis in the chick embryo, as well as their behavior in response to extended cell passages and at various periods in culture. Primary cultures derived from the telencephalic region of 3-day-old chick embryo (stage 19) exhibited intense staining for vimentin (Vim; indicative of immature glial phenotypes) throughout the 17-day culture period, transitioning to Vim-positive/glial fibrillary acidic protein (GFAP)-positive astroblasts after a single cell passage at 13 days in vitro (DIV). With subsequent passage (P; through P6), cell continued to coexpress Vim/GFAP with the occasional appearance of fibronectin (Fib). By P11, Vim staining was faint, whereas GFAP staining gained in intensity, indicating the presence of mature astrocytes. These cultures also featured significant activity of glutamine synthetase (GS), which increased slightly with both cell passage and days in culture, correlating well with immunocytochemical findings. The activity of 2'3'-cyclic nucleotide 3'-phosphohydrolase (CNP) remained low, indicating a low percentage of mature oligodendrocytes. Thus, embryonic day (E)3H glia cultures mature into astrocytes given sufficient time in culture. To obtain a stable population of glia at various stages of astrocytic differentiation, we immortalized and subcloned homogenous colonies of E3H glia precursors at specific stages of development. A cell suspension was electroporetically transfected with the pSV40neo gene for large T antigen (E3H.SV5). After 5 passages, the parent colonies consisted of a heterogeneous population of cells, most of which were vim and GFAP positive. Following subcloning, one line (colony 7) displayed the staining pattern of mature astrocytes. However, with advancing age in culture, staining for both vim and GFAP became increasingly faint. Compared with control (normal) cultures, transfected cells exhibited a significantly lower activity of GS that did not fluctuate with days in culture but decreased with advancing cell passage. Furthermore, CNP activity in E3H.SV5 colony 7 was approximately double that observed in normal cultures at the same cell passage. This observation suggests that the phenotype of transfected glia was less stable than that observed in normal glial cultures.
Canonical and non-canonical Wnts differentially affect the development potential of primary isolate of human bone marrow mesenchymal stem cells.

This study examines the role of Wnt signaling events in regulating the differential potential of mesenchymal stem cells (MSCs) from adult bone marrow (BM). Immunohistochemical analysis of BM revealed co-localization of Wnt5a protein, a non-canonical Wnt, with CD45+ cells and CD45− STRO-1+ cells, while Wnt3a expression, a canonical Wnt, was associated with the underlying stroma matrix, suggesting that Wnts may regulate MSCs in their niche in BM. To elucidate the role of Wnts in MSC development, adult human BM-derived mononuclear cells were maintained as suspension cultures to recapitulate the marrow cellular environment, in serum-free, with the addition of Wnt3a and Wnt5a protein. Results showed that Wnt3a increased cell numbers and expanded the pool of MSCs capable of colony forming unit — fibroblast (CFU-F) and CFU — osteoblast (O), while Wnt5a maintained cell numbers and CFU-F and CFU-O numbers. However, when cells were cultured directly onto tissue culture plastic, Wnt5a increased the number of CFU-O relative to control conditions. These findings suggest the potential dual role of Wnt5a in the maintenance of MSCs in BM and enhancing osteogenesis ex vivo. Our work provides evidence that Wnts can function as mesenchymal regulatory factors by providing instructive cues for the recruitment, maintenance, and differentiation of MSCs. J. Cell. Physiol. 212:817–826, 2007. © 2007 Wiley-Liss, Inc.
Numerical simulation of the slider air bearing problem of hard disk drives by two multidimensional upwind residual distribution schemes over unstructured triangular meshes

Abstract In this paper we present two multigrid numerical schemes over unstructured triangular meshes that solve the slider air bearing problem of hard disk drives. For each fixed slider attitude, the air bearing pressure is obtained by solving the generalized Reynolds equation. The convection part of the equation is modeled in one scheme by the PSI multidimensional upwind residual distribution approach and in the other scheme by the SUPG finite element approach cast in residual distribution form. In both schemes, a linear Galerkin method is used to discretize the diffusion terms. In addition, a non-nested multigrid iteration technique is used to speed up the convergence rate. Finally, the balanced steady state flying attitude of the slider subject to pre-applied suspension force and torques is obtained by a Quasi–Newton iteration method (Broyden's method), and the results of the numerical solutions are compared to each other and to experimental data.
Community structure analysis in big climate data

The analysis of climate data as a complex network has shown a great deal of promise over the last decade. Because of the massive size of the resulting network structure, much of the literature in this area has focused on the analysis of a single network snapshot generalized for a single period of time. Therefore, existing analysis methods typically focus on network properties instead of structural nature of the network to find interesting patterns. Data analysis and mining in complex climate networks at a higher temporal granularity, as a result, creates a challenging yet computationally prohibitive big data problem. In this paper, we extend the analysis of complex climate networks by studying their underlying community structures, an important property that is commonly exhibited in most complex networks. In particular, we first propose a new two-layer network model that captures community structures at both generalized and hierarchical levels where sub-communities are contained within the resulting generalized communities. Our two-layer network significantly reduces the complexity of modeling climate networks, and therefore reduces the computational complexity associated with analyzing big climate data. To mine meaningful climate patterns, we further extend this approach and suggest algorithms to find persistent communities that are stable over a long period of time. Our methods were tested on global air temperature data and we found signature communities that are verified by well known global temperature patterns. The results also produced some interesting discoveries related to known climate events such as the 1997/1997 El Nino and the eruption of Mt. Pinatubo in 1991.
Predicting more from less: Synergies of learning

Thanks to the ever increasing importance of project data, its collection has been one of the primary focuses of software organizations. Data collection activities have resulted in the availability of massive amounts of data through software data repositories. This is great news for the predictive modeling research in software engineering. However, widely used supervised methods for predictive modeling require labeled data that is relevant to the local context of a project. This requirement cannot be met by many of the available data sets, introducing new challenges for software engineering research. How to transfer data between different contexts? How to handle insufficient number of labeled instances? In this position paper, we investigate synergies between different learning methods (transfer, semi-supervised and active learning) which may overcome these challenges.
A coupled oscillators-based control architecture for locomotory gaits

This paper presents a bio-inspired central pattern generator (CPG) architecture for optimal control of locomotory gaits. The CPG circuit is realized as a coupled oscillator feedback particle filter. The collective dynamics of the filter are used to approximate a posterior distribution that is used to construct the optimal control input. The architecture is illustrated with the aid of a model problem involving locomotion of coupled planar rigid body systems, with two links. For this problem, the coupled oscillator feedback particle filter is designed and its control performance demonstrated in a simulation environment.
In-plane spatial encoding in MRI and its central role in determining contrast and artifact with RF echo planar techniques

Generating a magnetic resonance image requires that all three spatial dimensions of a spin system somehow get encoded into NMR signals. Although there are many ways this can be done, by far the most common is to restrict the excitation to a slice with the use of frequency-selective radio frequency (rf) pulses in the presence of a magnetic field gradient and to encode the remaining two spatial dimensions into echo signals with two mutually orthogonal „in-plane” gradients. In the standard scheme, spins along one in-plane dimension are localized by receiving the echo signal in the presence of a „read-out” gradient. Spins along the other in-plane dimension are localized with the use of „phase-encoding” gradients of different amplitudes applied for short periods prior to each readout. Just how these processes yield a data set whose two-dimensional (2D) Fourier transformation represents the spin density within the selected slice is a major topic of this discussion. A topical extension, to rf echo planar methods in which the usual phase-encoding process is accelerated with the use of multiple echoes, is also presented. The effects on image contrast and artifact when different echoes are used for distinct phase-encoding steps in the presence of T2 decay (the spin-spin relaxation time) are analyzed and illustrated.
LSm proteins form heptameric rings that bind to RNA via repeating motifs.

Members of the LSm family of proteins share the Sm fold – a closed barrel comprising five anti-parallel β strands with an α helix stacked on the top. The fold forms a subunit of hexameric or heptameric rings of ∼7nm in diameter. Interactions between neighboring subunits center on an anti-parallel interaction of the fourth and fifth β strands. In the lumen of the ring, the subunits have the same spacing as nucleotides in RNA, enabling the rings to bind to single-stranded RNA via a repeating motif. Eubacteria and archaea build homohexamers and homoheptamers, respectively, whereas eukaryotes use >18 LSm paralogs to build at least six different heteroheptameric rings. The four different rings in the nucleus that permanently bind small nuclear RNAs and function in pre-mRNA maturation are called Sm rings. The two different rings that transiently bind to RNAs and, thereby, assist in the degradation of mRNA in the cytoplasm and the maturation of a wide spectrum of RNAs in the nucleus are called LSm rings.
Repellency of methiocarb-treated grapes to three species of birds

Abstract Tests were conducted to evaluate the repellency of methiocarb-treated grapes to European starlings ( Sturnus vulgaris ), American robins ( Turdus migratorius ) and house finches ( Carpodacus mexicanus ). Birds were individually caged, and provided with grape bunches during a series of daily 5-h feeding trials, and repellency was determined by comparing damage done to the methiocarb-treated grapes with each bird's earlier damage to untreated grapes. A significant R 50 (the estimated concentration that repels 50% of the birds) of 7.3 g methiocarb per 1 water was found during the 1st day that starlings were exposed to treated grapes. However, during 4 subsequent days of exposure damage became quite variable while generally increasing to near pretreatment levels. During their 3rd day of exposure to methiocarb, a significant R 50 of 2.8 g/l was recorded for the robins, and repellency was more uniform during the course of the five treatment feeding trials than for either the starlings or finches. The most pronounced repellency was for the finches, which had significant R 50 's ranging from 0.3 to 0.9 g/l. The amount of damage caused by finches declined sharply between the 1st and 5th days of exposure to the repellent.
Adaptive Situation Awareness Using Visual Analytics

The accurate estimation of environment is a precursor to awareness of the situation around subject(s) of interest. It is imperative that awareness leads to better, improved and safer surroundings and in many cases averts disasters. Following clues from human cognitive nature there have been a significant progress in the development of situation awareness (SAW) models and its implementation in wide ranging industrial, medical and defense applications. The information collected, when utilized in hierarchical order of priority, allows for accurate decision making up to certain degree of confidence. The challenges faced in current applications are the dissemination of information and its demonstration to make artificially intelligent decisions when it goes beyond the perception or comprehension of human mind. In this paper a design methodology is detailed related to adaptive situation awareness (SAW), and the components that are required for its development. The features of intelligent visual analytics and its importance in the development of SAW are also explained. Finally an approach is laid out for arriving at an adaptive SAW with the help of visual analytics model in a bottom up approach, starting from data generation, fusion, logical search algorithm, protocol development and using mathematical modeling for probabilistic approach to a certainty based adaptive SAW model.