cssi/SciSciGPT-SciSciNet huggingface dataset:
Measurement of nucleoside kinases in crude tissue extracts

Abstract The measurements of deoxyadenosine kinase, adenosine kinase, and deoxycytidine kinase were examined in human placental cytosol to achieve a valid and reliable assay linear with time and protein. Our studies confirm the need to inhibit deaminase enzymes, since deoxyadenosine and deoxycytidine undergo extensive deamination and phosphorolysis. The use of a uniformly labeled nucleoside substrate introduced an artifact because the chromatographic behavior of the deoxyribose-1-phosphate, formed during the assay, was difficult to distinguish from the deoxynucleoside phosphate product. Accurate product identification was also essential. Finally, the substitution of GTP in place of ATP as the phosphate donor, the addition of a sulfhydryl reducing agent and a monovalent cation need to be considered when an assay is optimized. The use of these methods have lead to valid assays in placental cytosol that are linear with time and protein. Consideration of these important principles are necessary when establishing a valid and reliable nucleoside kinase assay in a crude tissue preparation.
Heterodyning far-infrared light using coherent photovoltaic effect

Summary form only given. There is great interest in development of a sensitive low-noise detector in the far-infrared (FIR) (10-100 /spl mu/m) range. The progress is impeded by a large dark current and associated thermal noise in the detectors, which significantly reduces their detectability. Detectability can be improved in the coherent or heterodyne schemes, where the sensitivity can be pushed to its quantum limit. Heterodyne detection in the 10.6-/spl mu/m range had been successfully implemented in quantum-well intersubband detectors (QWIPs). Therefore quite an effort has been directed toward development of the efficient local oscillators in the FIR range.
Transcriptional Regulation of C/EBPδ in G0 Growth-Arrested Mouse Mammary Epithelial Cells

Abstract Little is known about the control of cell cycle exit/G0 entry, or the regulation of genes that are expressed during G0. In this report we used primer extension analysis to demonstrate the high level of C/EBPδ mRNA expression in G0 growth-arrested HC11 mouse mammary epithelial cells and to identify the C/EBPδ transcription start site. The C/EBPδ gene transcription rate and promoter activity are both highly induced in G0 growth-arrested HC11 cells. The C/EBPδ gene promoter also exhibits G0-specific autoregulation. In contrast, the C/EBPδ promoter activity decreases in G0 growth-arrested NIH 3T3 cells. These data indicate that C/EBPδ is among a relatively small number of genes actively transcribed during G0 growth arrest. C/EBPδ may regulate the expression of genes implicated in the initiation or maintenance of mammary epithelial cell G0 growth arrest.
Intermediate Channeling on the Trifunctional β-Oxidation Complex from Pig Heart Mitochondria

The kinetic properties of the purified trifunctional β-oxidation complex (TOC) from pig heart mitochondria were analyzed with the aim of elucidating the functional consequence of having three sequentially acting enzymes of β-oxidation associated in one complex. The kinetic parameters of TOC and of the component enzymes of TOC, long-chain enoyl-CoA hydratase, long-chain 3-hydroxyacyl-CoA dehydrogenase, and long-chain 3-ketoacyl-CoA thiolase, were determined with substrates having acyl chains with 16 carbon atoms. Quantification by high performance liquid chromatography of intermediates formed during the degradation of 2-trans-hexadecanoyl-CoA to myristoyl-CoA and acetyl-CoA by TOC revealed the accumulation of 3-hydroxyhexadecanoyl-CoA, whereas 3-ketohexadecanoyl-CoA was undetectable. The observed rates of NADH and acetyl-CoA formation were higher than the theoretical rates calculated by use of the kinetic parameters and measured concentrations of intermediates. When the sequence of reactions catalyzed by TOC was inhibited by acetyl-CoA, the steady-state concentration of the 3-hydroxyacyl-CoA intermediate was not affected, whereas a small amount of 3-ketohexadecanoyl-CoA was detected. The differences between observed and predicted reaction rates and between measured and expected concentrations of intermediates are best explained by the operation of a channeling mechanism. As a consequence of intermediate channeling between the active sites on the complex, more coenzyme A is available in the mitochondrial matrix and metabolites like 3-ketoacyl-CoA thioesters, which are strong inhibitors of several β-oxidation enzymes, do not accumulate.
Modelling myoelectric interference patterns during movement.

Interpretation of myoelectric interference patterns during movement relies on suitably formulated models. In the review, various modelling approaches are described and discussed. The importance of incorporating the time lag between mechanical and electrical activities in models of myoelectric activity is underlined. It is suggested that a portion of electrical activity is not related to force production but represents muscle efforts at damping oscillations in the surrounding soft tissues.
Effect of Androgen and Estrogen Treatment on Hamster Liver and Kidney Estrogen 2-/4-Hydroxylase Activity*

The activity of microsomal estrogen 2-/4-hydroxylase enzyme (ESH), which mediates the formation of catechol estrogens, was determined in the hamster kidney and liver under different endocrine states and after treatment with diethylstilbestrol (DES) and 5α-dihydrotestosterone alone or in combination. Our results indicate that at least 64% of the renal ESH activity is localized in the kidney cortex. Employing either estrone or 17β-estradiol as subtrate, a significant decline in renal ESH activity was observed after castration, with estrone remaining the more active substrate. In contrast, hepatic ESH activity, which is about 2.0- to 2.5-fold higher than the kidney enzyme, was not altered after gonadectomy using either estrogen substrate. A further reduction in renal ESH activity was found in DES-treated castrated hamsters when estrone was used. Androgen treatment resulted in a nearly 2-fold increase in kidney ESH activity using either estrogen substrate. Animals treated concomitantly with DES and 5α-dihydro...
Nucleation and epitaxial growth of Cr crystals on stepped W surfaces with low-index facets

Abstract The nucleation and epitaxial growth of Cr overlayers and crystals have been studied by vapor depositing chromium onto thermally annealed W field electron emitters, which provide highly stepped substrates with low-index facets of various atomic configurations. Temperature and substrate morphology effects were identified and Cr/W epitaxial relationships were determined. In addition to the common Stranski-Krastanov (SK) nucleation mechanism (nucleation on top of a Cr overlayer) observed generally above ∼ 500 K, low temperature Cr nucleation and growth (∼300 K) was observed on the W{110} planes. This process proceeded via either the SK or Volmer-Weber (VW) (nucleation directly on the substrate) mechanisms, depending upon the Cr deposition geometry. The influence of oxygen contamination is identified and comparisons to recent Cr/W(100) and Cr/W(110) work are made.
Green's functions for antiferromagnetic polaritons. II. Scattering from rough surfaces.

The scattering of an incident electromagnetic wave from a semi-infinite antiferromagnet with a rough surface is treated using the classical Maxwell wave equations. We limit our discussion to scattering within polarizations perpendicular to the plane of incidence. We first calculate the roughness-induced scattering from a periodic grating and show how the grating can couple the incident wave to both the forward (+${k}_{x}$) and backward (-${k}_{x}$) traveling surface-polariton states. We also find that the grating can induce strong coupling to the Brewster-type ``leaky'' modes. Finally we consider scattering from a randomly varying surface and estimate the change in reflectivity due to roughness-induced scattering into surface-polariton states.
Teaching Generalized Pretend Play and Related Behaviors to Young Children With Disabilities

Children with disabilities play less often and demonstrate fewer varied pretend play behaviors than children with typical development. A multiple-probe design was used to examine the relation between teachers’ use of the system of least prompts and contingent imitation and the acquisition, maintenance, and generalization of pretend play and related behaviors by four children with disabilities. Results indicated the teachers’ use of the intervention package was functionally related to increases in the children’s frequency and diversity of pretend play and related behaviors. Children also maintained responses in sessions without prompts and generalized across toys and contexts. The findings replicate previous studies on adult prompting of pretend play and extend the literature by assessing generalization of children’s pretend play across contexts and measuring intervention and implementation fidelity. Overall, this study provides a strong argument for engaging in systematic instruction of play, including pr...
Long-term corticosteroid effect on lymphocyte and polymorphonuclear cell function in asthmatics

Abstract The effect of long-term alternate-day steroid administration on lymphocyte and polymorphonuclear cell (PMN) functions was studied in 10 steroid-dependent adult asthmatic patients. The duration of alternate-day prednisone usage ranged from 3 to 12 yr with an average of 6.7 ± 3.6 yr. Maintenance steroid dosage at the time of study ranged from 20 to 50 mg on alternate days, averaging 31 ± 8 mg. Prednisone caused marked lymphopenia, suppression of phytohemagglutin (PHA) lymphocyte transformation and PMN adherence 4 hr after ingestion. By 24 hr these measurements returned to normal or higher. These effects appeared at all doses between 20 and 50 mg of prednisone. In contrast, there was no statistically significant suppression of the total leukocyte count, total and active erythrocyte (E) rosette-forming lymphocytes, serum immunoglobulin concentrations, polymorphonuclear cell (PMN) phagocytosis, or delayed skin reactivity. We conclude that the acute effects of prednisone on lymphocyte and PMN function are transient and return to normal levels by 24 hr. The continued administration of beclomethasone dipropionate by inhalation did not interfere with the recovery of the transient leukocyte abnormalities induced by oral prednisone.
Statistical Methods for Mapping Multiple QTL

Since Lander and Botstein proposed the interval mapping method for QTL mapping data analysis in 1989, tremendous progress has been made in the last many years to advance new and powerful statistical methods for QTL analysis. Recent research progress has been focused on statistical methods and issues for mapping multiple QTL together. In this article, we review this progress. We focus the discussion on the statistical methods for mapping multiple QTL by maximum likelihood and Bayesian methods and also on determining appropriate thresholds for the analysis.
Resource Guide on Cyberbullying

Cyberbullying is a pressing issue for young people and school personnel. Helpful resources are available for victims of cyberbullying and their families as well as school professionals. Both electronic and published cyberbullying resources are presented along with statistics and helpful identification and prevention strategies.
A MICROSCOPIC SIMULATION MODEL FOR MERGING CONTROL ON A DEDICATED-LANE AUTOMATED HIGHWAY SYSTEM

Abstract The automated highway systems (AHS) are not designed as stand-alone transportation facilities. Drivers will by necessity drive from their origins to the AHS entrance, and from the AHS exit to their final destinations. Therefore, the AHS will affect other transportation facilities, and should be integrated with all other facilities in the transportation system. Interfaces create much of the congestion for today’s transportation systems. Likewise, AHS interfaces may cause a similar problem, due to either AHS interactions with conventional systems or internal limitations from AHS merging capabilities. If these problems exist, either the AHS or the conventional road network cannot function properly. Consequently, the system as a whole may break down and the AHS could potentially become a detriment to the overall transportation system. Clearly, not enough is known about the automated merging process to determine what conditions would lead to congestion at interface points. The current macroscopic analysis techniques assume parameters that are not applicable to an AHS, and no detailed AHS merging models have been developed and validated. This paper addresses the interface problem between an AHS, and conventional roadway. Specifically, it presents a microscopic simulation model for one scenario of the automated merging maneuver. The results of the model show that for low flows and conventional highway speeds, an one-lane AHS merging section with a dedicated automated entrance ramp has many similar characteristics as a two-lane conventional freeway with or without fixed-time ramp metering. However, when the conventional freeway starts to “break down” near its capacity, the AHS continues to perform with little delay. The model also validates that the minimum ramp length requirements are a function of the merging vehicle’s speed, the mainline vehicles’ speed, and the acceleration and deceleration rates of the merging vehicle.
Obsessive-compulsive disorder in children and adolescents: a review

Obsessive-compulsive disorder (OCD) is a common psychiatric illness that occurs across the entire life span. Although most research on OCD pertains to adults, studies of the disorder in children and adolescents have burgeoned over the last decade. A review of this literature suggests that OCD has a bimodal incidence pattern, with one peak of onset at approximately 10 years of age and another during adulthood, and that the juvenile and adult forms are equally prevalent. Important similarities and differences between the juvenile- and adult-onset forms of OCD can be seen: both show the same clinical phenotype, diagnostic nosology, and dose responsivity, but the early-onset disorder differs in being clearly male preponderant, more highly familial, and associated with a distinct pattern of comorbid psychopathology, including disruptive behavior and specific developmental disorders. These findings have implications both for clinical management and for future research, which could consider age of onset as an important factor in studies of all OCD patients.
Prolonged monitoring of ethinyl estradiol and levonorgestrel levels confirms an altered pharmacokinetic profile in obese oral contraceptives users

Abstract Background Pharmacokinetic (PK) parameters based on short sampling times (48 h or less) may contain inaccuracies due to their dependency on extrapolated values. This study was designed to measure PK parameters with greater accuracy in obese users of a low-dose oral contraceptive (OC) and to correlate drug levels with assessments of end-organ activity. Study Design Obese [body mass index (BMI) ���30 kg/m 2 ], ovulatory, otherwise healthy women ( n =32) received an OC containing 20 mcg ethinyl estradiol (EE)/100 mcg levonorgestrel (LNG) for two cycles. EE and LNG PK parameters were characterized for 168 h at the end of Cycle 1. During Cycle 2, biweekly outpatient visits were performed to assess cervical mucus, monitor ovarian activity with transvaginal ultrasound and obtain serum samples to measure EE, LNG, estradiol and progesterone levels. PK parameters were calculated and correlated with end-organ activity and compared against control samples obtained from normal and obese women sampled up to 48 h in a previous study. Standard determination of PK accuracy was performed, defined by the dependency on extrapolated values (���excess��� area under the curve of 25% or less). Results The mean BMI was 39.4 kg/m 2 (SD 6.6) with a range of 30���64 kg/m 2 . Key LNG PK parameters were as follows: clearance, 0.52 L/h (SD 0.24); half-life, 65 h (SD 40); area under the curve (AUC), 232 h*ng/mL (SD 102); and time to reach steady state, 13.6 days (SD 8.4). The majority of subjects had increased ovarian activity with diameter of follicles ���8 mm ( n =25), but only seven women had follicles ���10 mm plus cervical mucus scores ���5. Evidence of poor end-organ suppression did not correlate with the severity of the alterations in PK. As compared to historical normal and obese controls (48-h PK sampling), clearance, half-life, AUC and time to reach steady state were found to be significantly different (p���.05) in obese women undergoing a longer duration of PK sampling (168 h). Longer sampling also improved PK accuracy for obese women (excess AUC 20%) as compared to both normal and obese controls undergoing shorter sampling times (48 h) with excess AUCs of 25% and 50%, respectively. Conclusions Obesity results in significant alterations in OC steroid PK parameters, but the severity of these alterations did not correlate with end-organ suppression. A longer PK sampling interval (168 h vs. 48 h) improved the accuracy of PK testing.
Presentation and management of Morgagni hernias in adults : a review of 298 cases

Background Morgagni hernias are a very rare form of diaphragmatic hernias. No robust studies have been performed to show the true natural history of this disease process. This study aimed to summarize clinically relevant data with respect to Morgagni hernias in adults. These data should help surgeons workup, diagnose, and treat Morgagni hernias in adult patients.
On existence of a quadratic comparison function for random weighted averaging dynamics and its implications

In this paper we study the stability and limiting behavior of discrete-time deterministic and random weighted averaging dynamics. We show that any such dynamics admits infinitely many comparison functions including a quadratic one. Using a quadratic comparison function, we establish the stability and characterize the set of equilibrium points of a broad class of random and deterministic averaging dynamics. This class includes a set of balanced chains, which itself contains many of the previously studied chains. Finally, we provide some implications of the developed results for products of independent random stochastic matrices.
Mechatronics and smart structures: emerging engineering disciplines for the third millennium

Abstract This paper tackles the impact that Mechatronics and Smart Structures disciplines have on the engineering education in the new millennium. Mechatronics is an emerging engineering area that will likely alter the fundamental nature of engineering education in the disciplines of electrical and mechanical engineering. It can provide an academic model for developing multi-disciplinary programs within the engineering college departmental structure that is historically based on the traditional engineering disciplines. Mechatronics integrates the classical fields of mechanical engineering, electrical engineering, computer engineering, and information technology to establish basic principles for a contemporary engineering design methodology. A mechatronics concentration area in the engineering curriculum would support the synergistic integration of precision mechanical engineering, electronics control, and systems thinking into the design of intelligent products and processes. Smart Structures, a. k. a. Adaptive Structures, a. k. a. Adaptronics, is an emerging engineering field with multiple defining paradigms. One definition is based upon a technology paradigm: “the integration of actuators, sensors, and controls with a material or structural component”. Multi-functional elements form a complete regulator circuit resulting in a novel structure displaying reduced complexity, low weight, high functional density, as well as economic efficiency. Another definition is based upon a science paradigm in an attempt to capture the essence of biologically inspired materials by addressing the goal as creating material systems with intelligence and life-like features integrated in the microstructure of the material system to reduce mass and energy and produce adaptive functionality. Their basic characteristics of efficiency, functionality, precision, self-repair, and durability continue to fascinate designers of engineering structures today.
Seismic interferometry and estimation of the Green’s function using Gaussian beams

This study investigates seismic interferometry in which the Green’s function is estimated between two receivers by cross-correlation and integration over sources. For smoothly varying source strengths, the dominant contributions of the correlation integral come from the stationary phase directions in the forward and backward directions from the alignment of the two receivers. Gaussian beams can be used to evaluate the correlation integral and concentrate the amplitudes in a vicinity of the stationary phase regions instead of completely relying on phase interference. Several numerical examples are shown to illustrate how this process works. The use of Gaussian beams for the evaluation of the correlation integral results in stable estimates, and also provides physical insight into the estimation of the Green’s function based on seismic interferometry.
Student-Teacher Relationships Matter: Moderating Influences Between Temperament and Preschool Social Competence

Ecological approaches to preschool assessment, which consider both within-child and environmental variables, are considered best practice for school psychologists. This study employs such a model to investigate the interactive influence of child temperament and student–teacher relationship quality on peer play behaviors. Parents of 44 preschool children (25 girls, 19 boys) ranging in age from 40 to 68 months (mean [M]=53.00) and primarily White (92.9%) provided ratings of their children’s temperaments on the Behavioral Style Questionnaire. Their teachers completed the Student–Teacher Relationship Scale and the Penn Interactive Peer Play Scale. Results indicate that (a) student–teacher relationships characterized by low conflict and low dependence are associated with less disruptive peer play, and (b) the association between temperament and disruptive play is attenuated in low conflict student–teacher relationships. Implications for school psychologists include the importance of student–teacher relationships in the context of preschool assessment and intervention planning.
Salivary Elimination of Cyclophosphamide in Man

: A total of 25 plasma and saliva samples were obtained from three hospital inpatients upon intravenous short-time infusion of cyclophosphamide; total doses infused ranged from 5.3 to 13.3 mg/kg. Despite interindividual variations, a correlation was found for plasma-to-saliva ratio of 1.61 ± 0.53 (S.D.). Our saliva-to-plasma ratio of 0.62 is in agreement with a recently reported5 ratio of 0.77. The ratio stayed constant throughout the observation period (0.05 to 8.4 hours), indicating that the noninvasive method of saliva sampling seems to be a useful approach in cyclophosphamide drug concentration monitoring in patients.
Phase-oscillator computations as neural models of stimulus–response conditioning and response selection ☆

Abstract The activity of collections of synchronizing neurons can be represented by weakly coupled nonlinear phase oscillators satisfying Kuramoto’s equations. In this article, we build such neural-oscillator models, partly based on neurophysiological evidence, to represent approximately the learning behavior predicted and confirmed in three experiments by well-known stochastic learning models of behavioral stimulus–response theory. We use three Kuramoto oscillators to model a continuum of responses, and we provide detailed numerical simulations and analysis of the three-oscillator Kuramoto problem, including an analysis of the stability points for different coupling conditions. We show that the oscillator simulation data are well-matched to the behavioral data of the three experiments.
Understanding alexithymia and language skills in children: implications for assessment and intervention.

Purpose This article reviews the construct of alexithymia and its relationship to language impairment. Method The article includes a review of the literature on emotional competence, trauma effects...
Contractile Filopodia and in Vivo Cell Movement in the Tunic of the Ascidian, Botryllus Schlosseri

SUMMARY The in vivo movement of one class of cells in the tunic of the ascidian Botryllns schlosseri has been analysed using differential interference optics and time-lapse cinematography. Long (up to 200/tm), thin (0-35-0-5 /tm diameter) filopodia radiate from the cell-body into the matrix of the tunic. Movement of the cell-body consists of a series of short, jerky displacements with frequent changes in direction between successive displacements. The net displacement of the cell may be extremely small when the displacements are short and frequently change direction, or considerable when successive displacements show a persistence of direction (up to 114/tm in 60 min). Deformation of the elastic cuticle covering the tunic at points of attachment of the filopodia has been used to record qualitatively changes in tension in the filopodia. Correlation of the changes in tension with changes in length of the filopodia and movement of the cell-body have permitted the following conclusions. Active contractions of filopodia (i.e. increase in tension during shortening) stretch and move the cell-body. These movements exert a force on trailing or opposing filopodia. Relaxations of filopodia (i.e. decrease in tension during lengthening) result in small movements of the cell-body due to the recoil of tension in the cell-body and opposing filopodia. The position of the cell-body in space at any one instant in time is therefore the resultant of the forces developed in all the filopodia. Movement results from unilateral modulation of the tension developed in the filopodia. Active contractions play a more significant role in movement than relaxations.
Visions and Reality: Reconsidering the Creation and Development of Lowell's National Park, 1966–1992

Abstract For more than four decades, historians, historic preservationists, journalists, and public officials have debated the purpose and appropriateness of a national park in Lowell, Massachusetts. This article, written by the first NPS historian in Lowell, builds on existing literature and interprets the founding and early development of Lowell National Historical Park in the context of changing national politics. It locates the concept for the park in the Great Society, documents the contested debate over the park9s founding in the 1970s, and argues that the park developed very differently than planned during the radically changed political environment of the 1980s.
AN ALGORITHM FOR FINDING NOUN PHRASE CORRESPONDENCES IN BILINGUAL CORPORA

The paper describes an algorithm that employs English and French text taggers to associate noun phrases in an aligned bilingual corpus. The taggers provide part-of-speech categories which are used by finite-state recognizers to extract simple noun phrases for both languages. Noun phrases are then mapped to each other using an iterative re-estimation algorithm that bears similarities to the Baum-Welch algorithm which is used for training the taggers. The algorithm provides an alternative to other approaches for finding word correspondences, with the advantage that linguistic structure is incorporated. Improvements to the basic algorithm are described, which enable context to be accounted for when constructing the noun phrase mappings.
A thrombospondin homologue in Drosophila melanogaster: cDNA and protein structure.

Abstract The cDNA of a thrombospondin homologue in Drosophila melanogaster (DTSP) has been sequenced, and structural features of the translated protein analyzed. Thrombospondin proteins had previously been identified only in vertebrates, including human and mouse. Comparison with the genomic sequence revealed that the DTSP gene is divided into 13 exons; The translation initiation site is in exon 2. The transcription start site was analyzed using a PCR procedure, and the longest transcripts were found to initiate about 300 bp 5′ of the predicted start site. The open reading frame of the DTSP cDNA encodes a protein that has 1060 amino acid residues. The polypeptide is composed of domains or repeats characteristic of the TSP3/TSP4/COMP subfamily of thrombospondin proteins: Amino-terminal domain, four Type II repeats, seven Type III repeats, carboxyl-terminal domain. The protein is highly acidic, particularly in the region of Type III repeats, with an Asp + Glu content of 15.8%. A signal peptide was detected at the N-terminus, which indicates that DTSP, like other TSPs, functions as an extracellular protein. Ten Asn residues were identified as potential glycosylation sites. Alignment of the amino acid sequences of the Drosophila TSP with human TSP1–TSP4 and COMP demonstrated a high degree of homology between the four Type II repeats, seven Type III repeats, and C-terminal domain.
Joint performance study of channel estimation and multiuser detection for uplink long-code CDMA systems

Although numerous channel estimation and multiuser detection approaches have appeared for long-code uplink CDMA systems, joint performance study of channel estimators and symbol detectors remains largely open. In this paper, we construct three typical symbol-level linear receivers upon existing channel estimation method, known as zero-forcing (ZF), minimum mean-square-error (MMSE), and RAKE receivers, for symbol detection. Since the channel estimation error is rippled to the linear receivers, performance of all receivers is thus jointly analyzed with the channel estimator from a perturbation perspective. Extensive simulation examples involving different communication environments demonstrate high consistency between our analysis and experimental results.
Large Grain Size Stochastic Optimization Alignment

DNA sequence alignment is a critical step in identifying homology between organism. The most widely used alignment program, ClustalW is known to suffer from the local minima problem, where suboptimal guide trees produce incorrect gap insertions. The optimization alignment approach, has been shown to be effective in combining alignment and phylogenetic search in order to avoid the problems associated with poor guide trees. The optimization alignment algorithm operates at a small grain size, aligning each tree found, wasting time producing multiple sequence alignments for suboptimal trees. This research develops and analyzes a large grain size algorithm for optimization alignment that iterates through steps of alignment and phylogeny search, thus improving the quality of guide trees used for computation of multiple sequence alignments and eliminating computation of multiple sequence alignments for sub-optimal guide trees. Local minima are avoided by the use of stochastic search methods. Large Grain Size Stochastic Optimization Alignment (LGA) exploits the relationship between phylogenies and multiple sequence alignments, and in so doing achieves improved alignment accuracy. LGA is licensed under the GNU General Public License. Source code and data sets are publicly available at http://csl.cs.byu.edu/lga/
Synthesis of an ethylene glycol cross-linked amino acid

Abstract Synthesis of an ethylene glycol-containing amino acid, (2R,9S)-N2-Cbz-N9-Boc,2,9-diamino-4,7-dioxadecanedioic acid 1-phenacyl 10-methyl diester 1, was studied through direct alkylation of N-Boc-L-serine and through BF3-catalyzed ring opening of N-acylaziridinecarboxylates.
The prognostic significance of lymphovascular space involvement in patients with uterine-confined endometrioid endometrial cancer.

Copyright © 2012. Korean Society of Obstetrics and Gynecology Endometrial cancer is the most common gynecological malignancy in the Western world. For patients with a uterine-confi ned earlystage endometrial carcinoma, the infl uence of prognostic factors such as patient age, the tumor grade, and the depth of invasion are well-recognized [1]. The presence of lymphovascular space involvement (LVSI) has also been shown to be an independent prognostic factor in several studies, yet its association with recurrence was not shown on the multivariate analysis in other studies [2]. LVSI was associated with compromised survival in patients who are at clinical stages I and II, but not in patients at surgical stages I or II [3]. LVSI has been described as a predictor for nodal metastases or ORIGINAL ARTICLE
Defining the Role of Phosphomethylethanolamine N-Methyltransferase from Caenorhabditis elegans in Phosphocholine Biosynthesis by Biochemical and Kinetic Analysis †

In plants and Plasmodium falciparum, the synthesis of phosphatidylcholine requires the conversion of phosphoethanolamine to phosphocholine by phosphoethanolamine methyltransferase (PEAMT). This pathway differs from the metabolic route of phosphatidylcholine synthesis used in mammals and, on the basis of bioinformatics, was postulated to function in the nematode Caenorhabditis elegans. Here we describe the cloning and biochemical characterization of a PEAMT from C. elegans (gene, pmt- 2; protein, PMT-2). Although similar in size to the PEAMT from plants, which contain two tandem methyltransferase domains, PMT-2 retains only the C-terminal methyltransferase domain. RNA-mediated interference experiments in C. elegans show that PMT-2 is essential for worm viability and that choline supplementation rescues the RNAi-generated phenotype. Unlike the plant and Plasmodium PEAMT, which catalyze all three methylations in the pathway, PMT-2 catalyzes only the last two steps in the pathway, i.e., the methylation of phosphomonomethylethanolamine (P-MME) to phosphodimethylethanolamine (P- DME) and of P-DME to phosphocholine. Analysis of initial velocity patterns suggests a random sequential kinetic mechanism for PMT-2. Product inhibition by S-adenosylhomocysteine was competitive versus S-adenosylmethionine and noncompetitive versus P-DME, consistent with formation of a dead-end complex. Inhibition by phosphocholine was competitive versus each substrate. Fluorescence titrations show that all substrates and products bind to the free enzyme. The biochemical data are consistent with a random sequential kinetic mechanism for PMT-2. This work provides a kinetic basis for additional studies on the reaction mechanism of PEAMT. Our results indicate that nematodes also use the PEAMT pathway for phosphatidylcholine biosynthesis. If the essential role of PMT-2 in C. elegans is conserved in parasitic nematodes of mammals and plants, then inhibition of the PEAMT pathway may be a viable approach for targeting these parasites with compounds of medicinal or agronomic value.
Hopfield neural networks, and mean field annealing for seismic deconvolution and multiple attenuation

We describe a global optimization method called mean field annealing (MFA) and its application to two basic problems in seismic data processing: Seismic deconvolution and surface related multiple attenuation. MFA replaces the stochastic nature of the simulated annealing method with a set of deterministic update rules that act on the average value of the variables rather than on the variables themselves, based on the mean field approximation. As the temperature is lowered, the MFA rules update the variables in terms of their values at a previous temperature. By minimizing averages, it is possible to converge to an equilibrium state considerably faster than a standard simulated annealing method. The update rules are dependent on the form of the cost function and are obtained easily when the cost function resembles the energy function of a Hopfield network. The mapping of a problem onto a Hopfield network is not a precondition for using MFA, but it makes analytic calculations simpler. The seismic deconvoluti...
Oxidative Stress and Lower Urinary Tract Dysfunctions Primarily Found in Women

The incidence of lower urinary tract dysfunctions (LUTDs) in women increases with age. These dysfunctions include incontinence, recurrent urinary bladder infection, and poor bladder and urethral contraction. There is a corresponding progressive decrease in mean circulating estrogen as women age. We have data indicating that the rate at which LUTDs develop and progress is directly related to the decrease in circulating estrogen. Our studies on rabbits indicate that low circulating estrogen mediates a de crease in blood flow to the bladder and urethra. This in turn results in mucosal and smooth muscle hypoxia and the generation and release of free radicals. The end result is slow progressive oxidation damage of cellular and subcellular membranes (protein, lipids, and phospholipids), which relates directly to the etiology of age-related progressive LUTD. Estrogen administration to ovariectomized rabbits reverses these effects while causing smooth muscle hypertrophy, mucosal hyperplasia, increased vascularity and blood flow, fully oxygenated tissue, and reduced oxidative damage.
Risk factors for early work disability in systemic lupus erythematosus: results from a multicenter study.

Objective. To study the risk factors for early work disability in systemic lupus erythematosus (SLE). Methods. A sample of 159 SLE patients who had been employed at some time since diagnosis was drawn from a multicenter study of outcome in SLE. Disease activity, organ damage, education, income, source of health insurance, and work-related factors were measured in a standardized interview. Work disability was defined by patient self-report of not working because of SLE. The outcome measure was current work status. Seven patients were excluded from the analysis because their choice not to work was unrelated to SLE. Results. An average of 3.4 years after diagnosis, 40% had quit work completely, and job modification was substantial. Univariate analysis (chi-square and t-test) showed that significant predictors of early work disability included having a high school education or less, receiving Medicaid or having no health insurance, having a job which required more physical strength, having an income below poverty level, and having greater disease activity at diagnosis. In multivariate models, significant predictors were education level (P = 0.0004), higher physical demands of the job (P = 0.0028), and higher disease activity at diagnosis (P = 0.0078). Race, sex, cumulative organ damage at diagnosis, and disease duration were not significant. Conclusion. Early work disability in SLE is strongly associated with some sociodemographic factors that might be amenable to intervention.
Colonial "Reformation" in the Highlands of Central Sulawesi, Indonesia, 1892-1995

Colonial "Reformation" in the Highlands of Central Sulawesi, Indonesia, 1892-1995. Albert Schrauwers. Toronto: University of Toronto Press, 2000. 279 pp.
[Non]-deterministic dynamics in cells: From multistability to stochastic switching

I will discuss the interplay between “traditional” deterministic dynamics and stochastic effects in live cells. The main example the lac operon, a set of self-promoting genes, which, together with the enzymes they express, act as a hysteretic switch. Stochastic simulations of the same system predict spontaneous, random switching by individual cells. This behavior can be well described by a simple abstraction. In a broader context, we review a few examples where stochasticity leads to useful and quantifiable behavior that amounts to a hedging strategy on the level of a population of cells. Finally, we describe stochastic simulations of systems with spatial structure, a field with applications from cancer to swarm robotics.
Effects of package design on top PoP package warpage

In recent years, Package on Package (PoP), in which a top memory packaging system is connected to a bottom logic package via solder joint, is a System-in-Package (SiP) solution adopted by more and more component manufacturers. To guarantee the yield and reliability of the solder joint between the top package and bottom package, mechanical compliance between these two packages is crucial during package stacking. Therefore package warpage needs to be understood and controlled to meet certain target. Due to the complexity of mechanical structures with multi dies and material behaviors of substrate, molding compound and die attach film, package design to meet specific and tight warpage requirement is very challenging, especially when the packaging technology is developed by an envelope approach. Design parameters including substrate design property, die stacking configuration, and package size of the top SiP package play very important role in warpage performance. In this paper, the effects of various packaging design parameters on warpage are studied through comprehensive experiment, modeling and simulation. The findings and results provide some clues and guideline for design for warpage, which can reduce the product's time to market (TTM).
Are Periventricular Lesions Specific for Multiple Sclerosis

Background: The presence of periventricular lesions (PVL) on MRI scans is part of the revised McDonald multiple sclerosis (MS) diagnostic criteria. However, PVL can be found in other neurological diseases including stroke and migraine. Migraine is highly prevalent in patients with MS. Objective: To determine if PVL are specific for patients with MS compared to stroke and migraine. Methods: We studied patients diagnosed with clinically isolated syndrome (CIS), relapsing-remitting MS (RRMS), migraine, and ischemic stroke. The number, location and the volume of PVL were identified on brain MRI scans and analyzed. Results: The number and volume of PVL adjacent to the body and the posterior horn of the lateral ventricles were significantly increased on fluid-attenuated inversion recovery MRI in RRMS compared to migraine. There were no significant differences in the total number and volume of PVL in ischemic stroke patients compared to the agematched RRMS patients nor in the number and volume of PVL adjacent to the anterior and temporal horns of the lateral ventricles on FLAIR images in migraine compared to CIS or RRMS. Conclusion: In contrast to PVL adjacent to the body and the posterior horn of the lateral ventricles, PVL adjacent to the anterior and temporal horns of the lateral ventricles may not be specific for CIS/RRMS when compared to migraine, the disease highly prevalent among patients with MS. PVL are not specific for MS when compared to ischemic stroke.
3-Hydroxyanthranilic acid metabolism. V. Distribution of enzyme system in animal tissues.

SummaryA survey of various tissues of the rat; and of beef and pork liver and kidney was made for the presence of the enzyme system that converts 3-hydroxyanthranilic acid to quinolinic acid. It was found that rat and pork liver homogenates quantitatively convert 3-hydroxyanthranilic acid to quinolinic acid. Beef liver also contains this enzyme system, but not all of the substrate metabolized could be accounted for as quinolinic acid. Rat, pork and beef kidney likewise contain the enzyme system but again not all of the 3-hydroxyanthranilic acid metabolized was found by the quinolinic acid assay. Spleen, muscle, brain, pancreas and testis of rats either do not contain the enzyme system or contain it in very small quantities. No evidence was obtained to indicate that the intermediate compound previously described had accumulated to account for the lower production of quinolinic acid by these preparations.
Simulating the effect of grain boundaries on microstructurally small fatigue crack growth from a focused ion beam notch through a three-dimensional array of grains

Abstract Microstructurally small crack (MSC) growth strongly depends on local microstructure and often displays oscillatory character in terms of crack growth rate (da/dN) as a function of the conventional stress intensity range due to crack tip/grain boundary interactions of MSCs. A fatigue indicator parameter (FIP)-based MSC growth model is presented for high temperature MSC growth in polycrystalline Ni-base superalloy IN100 that takes into account crack tip/grain boundary interaction. An expression for FIP evolution is evoked based on a sequence of finite element simulations for stationary cracks. The MSC growth model was fit to experiments within the context of a simple 1D crack growth model and then applied to model 3D crack growth from a simulated focused ion beam (FIB) notch. Simulations showed that the MSC growth rate became less oscillatory as the MSC front sampled more grains, and eventually converged to the LEFM response with further crack extension.
Characterization of Coumatetralyl in Whole Blood by Liquid Chromatography-Mass Spectrometry with Atmospheric Pressure Chemical Ionization Interface

A method is presented for characterization of coumatetralyl in whole blood by high performance liquid chromatography-mass spectrometry with an atmospheric pressure chemical ionization interface(HPLC-APCI MS).Coumatetralyl in whole blood was extracted by ethyl acetate.Satisfactory separation was achieved on Zorbax XDB C_(18) column(150 mm×4.6 mm×5 μm) using a mobile phase consisting of CH_3OH-0.1% HAc(65∶35 by volume).Ionization was performed in the APCI(+) mode and quantitative analysis was carried out using the extracted ion chromatography(EIC) mode at m/z 293~+.The linear range was 0.30-100.0 μg/L and the limit of quantification was found to be 0.30 μg/L.The extraction recoveries were between 94%-105% with relative standard deviations of less than 10%.This method was sensitive,fast,and accurate in characterizing trace coumatetralyl in whole blood and can be carried out in the diagnosis of clinically poisoned patients.
Approach to Pediatric Patients with UTI in the PICU.

Urosepsis and UTI are common causes and comorbidities in children admitted to the pediatric intensive care unit (PICU). Risk factors for morbidity and mortality in pediatric patients include young age (
Displacement of housekeeping proteasome subunits by MHC-encoded LMPs: a newly discovered mechanism for modulating the multicatalytic proteinase complex.

Abstract The degradation of cytoplasmic antigens to peptides presented by class I MHC molecules is thought to be mediated by the ubiquitin/proteasome pathway. Support for this view came from our observation that the subunit composition of proteasomes can be changed by interferon-gamma (IFN-gamma) treatment. Thereby two subunits, LMP2 and LMP7, which are encoded in the MHC class II region, are incorporated into the proteasomal complex, whereas other subunits disappear. In the experiments reported in this communication we studied the subunit changes occurring in cell lines where the expression of LMP2 or LMP7 can be regulated individually either by IFN-gamma induction or by applying a new system to control the expression of transfected LMPs. In both situations LMP2 induction leads exclusively to the disappearance of housekeeping subunit 2, whereas LMP7 affects only subunit 10. Subunit 2 was found to be 76% homologous to LMP2. Since incorporation of LMP2 into the proteasomal complex prevents processing of the subunit 2 precursor, we conclude that LMP2 displaces subunit 2 during assembly. Subunit displacement is most likely a general mechanism to modulate the catalytic activity of the proteasomal complex without changing its structure. Furthermore, the controlled incorporation of transfected subunits into the complex offers a new approach to study proteasome function in vivo.