cssi/SciSciGPT-SciSciNet huggingface dataset:
TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles

Motivation: ChIP-seq and ChIP-chip experiments have been widely used to identify transcription factor (TF) binding sites and target genes. Conventionally, a fairly ‘simple’ approach is employed for target gene identification e.g. finding genes with binding sites within 2 kb of a transcription start site (TSS). However, this does not take into account the number of sites upstream of the TSS, their exact positioning or the fact that different TFs appear to act at different characteristic distances from the TSS. Results: Here we propose a probabilistic model called target identification from profiles (TIP) that quantitatively measures the regulatory relationships between TFs and target genes. For each TF, our model builds a characteristic, averaged profile of binding around the TSS and then uses this to weight the sites associated with a given gene, providing a continuous-valued ‘regulatory’ score relating each TF and potential target. Moreover, the score can readily be turned into a ranked list of target genes and an estimate of significance, which is useful for case-dependent downstream analysis. Conclusion: We show the advantages of TIP by comparing it to the ‘simple’ approach on several representative datasets, using motif occurrence and relationship to knock-out experiments as metrics of validation. Moreover, we show that the probabilistic model is not as sensitive to various experimental parameters (including sequencing depth and peak-calling method) as the simple approach; in fact, the lesser dependence on sequencing depth potentially utilizes the result of a ChIP-seq experiment in a more ‘cost-effective’ manner. Contact: ude.elay@nietsreg.kram Supplementary Information: Supplementary data are available at Bioinformatics online.
Modeling and Simulation for Control in Carding

The purpose of this work is to further study the transfer function model for carding introduced in a previous paper. Our goal is to develop mathematical and computational tools that will ultimately lead to the design of real-time controllers for carding. In this paper, we discuss a linear, time-variant version of the model presented for one carding group. We also present a reduced order, linear model and use it to build a linear estimator (observer) as part of a full-state feedback controller design. Computer sim ulations and experimental results are shown.
The effectiveness of antibiotic activity of penicillin attached to expanded poly(tetrafluoroethylene) (ePTFE) surfaces: a quantitative assessment.

Recent studies identified and established a platform of polymer surface modifications allowing the attachment of penicillin (PEN) to expanded poly(tetrafluoroethylene) (ePTFE) surfaces. The effectiveness of this approach was accomplished by creating surfaces with chemically attached PEN that prevent the proliferation of microbes. In this study, quantitative assessments of PEN effectiveness attached to ePTFE were conducted. Using variable-angle attenuated total reflectance (ATR-FTIR) spectroscopy, the volume concentration changes of PEN were determined as a function of depth from the ePTFE surface. At depths ranging from 0.2 to 1.2 μm from the surface, PEN concentration levels decrease from 8.85 to 3.33 μg/m3. Assessments of concentration levels of the colony forming units (CFUs) of Staphylococcus aureus bacteria as a function of contact time with the penicillin-polyethylene glycol spacer separated by maleic anhydride ePTFE (PEN-PEG-MA-ePTFE) surfaces showed profound effectiveness of PEN in preventing micr...
Quasi-chemical study of Be2+(aq) speciation

Abstract Be 2+ (aq) hydrolysis can to lead to the formation of multi-beryllium clusters, but the thermodynamics of this process has not been resolved theoretically. We study the hydration state of an isolated Be 2+ ion using both the quasi-chemical theory of solutions and ab initio molecular dynamics. These studies confirm that Be 2+ (aq) is tetra-hydrated. The quasi-chemical approach is then applied to then the deprotonation of Be(H 2 O) 4 2+ to give BeOH(H 2 O) 3 + . The calculated p K a of 3.8 is in good agreement with the experimentally suggested value around 3.5. The calculated energetics for the formation of [Be·OH·Be] 3+ are then obtained in fair agreement with experiments.
Directed Extended Dependency Analysis for Data Mining

Extended dependency analysis (EDA) is a heuristic search technique for finding significant relationships between nominal variables in large data sets. The directed version of EDA searches for maximally predictive sets of independent variables with respect to a target dependent variable. The original implementation of EDA was an extension of reconstructability analysis. Our new implementation adds a variety of statistical significance tests at each decision point that allow the user to tailor the algorithm to a particular objective. It also utilizes data structures appropriate for the sparse data sets customary in contemporary data mining problems. Two examples that illustrate different approaches to assessing model quality tests are given in this paper.
A multi-stage decoding strategy for the multiple antenna system

The original detection algorithm for the well known vertical Bell Laboratories layered space-time (V-BLAST) architecture for multiple antenna systems is based on the differential feedback equalization (DFE) principle. To improve the error performance of the V-BLAST system, a new decoding algorithm, based on the divide and conquer strategy, is proposed. The algorithm uses a recursive method to find the estimate for the transmitted symbol vector. The transmitted vector is divided into smaller subvectors, which are estimated recursively by further subdivision. The estimate of the smallest subvector (symbol) is obtained in a relatively straightforward manner. These subvectors are successively combined to obtain finally the estimate of the complete transmitted vector. We compare the new method with existing methods. It can be seen that the new method gives significant SNR improvement over other methods, at the cost of some added computation.
Spiral-in/out BOLD fMRI for increased SNR and reduced susceptibility artifacts.

BOLD fMRI is hampered by dropout of signal in the orbitofrontal and parietal brain regions due to magnetic field gradients near air-tissue interfaces. This work reports the use of spiral-in trajectories that begin at the edge of k-space and end at the origin, and spiral in/out trajectories in which a spiral-in readout is followed by a conventional spiral-out trajectory. The spiral-in trajectory reduces the dropout and increases the BOLD contrast. The spiral-in and spiral-out images can be combined in several ways to simultaneously achieve increased signal-to-noise ratio (SNR) and reduced dropout artifacts. Activation experiments employing an olfaction task demonstrate significantly increased activation volumes due to reduced dropout, and overall increased SNR in all regions.
Using collaborative learning teams to decode disciplines: Physiology and history

This chapter addresses the logistical considerations for the use of collaborative learning in the Decoding the Disciplines model and presents twelve principles for successfully using teamwork in the classroom and several assessments of the efficacy of the group process.
Effect of low-protein diets on growth performance and body composition of broiler chicks

Three experiments were conducted to investigate effects of dietary manipulations to improve growth performance and whole-body composition of broiler chicks fed low-protein diets supplemented with crystalline amino acids. In all experiments, male chicks (1 d old) were fed a common corn-soybean meal diet (23% CP) for 7 d and subsequently allotted to treatment diets in a completely randomized design (10 chicks per floor pen, six replications). Chicks had free access to the isoenergetic diets (3,200 kcal MEn/kg) for 2 wk, after which chicks were weighed and then fasted for 24 h, and the whole-body DM, N, and ether extract contents of two chicks per pen (and six baseline chicks) were determined. In Experiment 1, Gln or Asn replaced 1% triammonium citrate in the low-protein diet (19% CP). In Experiments 2 and 3, dietary concentrations of crystalline essential and nonessential amino acids, respectively, were increased incrementally in the low-protein diets (19 to 20% CP). In all experiments, chicks fed low-protein diets grew slower, used feed less efficiently, and retained less N and more ether extract than chicks fed the control diets (P < or = 0.05), despite additions of crystalline Gln or Asn and despite increased dietary concentrations of crystalline essential and nonessential amino acids. Chicks fed low-protein diets excreted less N (P < 0.001) than did chicks fed the high-protein diets, and N excretion increased linearly (P < 0.001) with N intake. In summary, low-protein diets failed to support equal growth performance to that of high-protein control diets.
Modification of Transferred Training Programmes for Multinational Chain Hotels in Korea

Transfer of training programmes between countries has created a circumstance that enhances the knowledge and skills of human resources in developing or underdeveloped countries along with the influence of globalisation in recent decades. The purpose of the study was to explore the hotels in Korea. The study was based on both qualitative and quantitative methods. A questionnaire was sent to training managers of all the multinational chain hotels in Korea. In addition, telephone interviews were conducted with the training managers of these hotels. The cross-case analysis revealed that the transfer of training programmes had certain patterns of modification shaped by the interacting factors in a three-level hierarchy: cultural and technical, organisational, and modifiers’ personal level. Each level also was found to have a subset of factors influencing the modification patterns. Future research is recommended to investigate the framework of the study in other countries and industries.
European Integration: Trade Data and Measurement Problems

Savage and Deutsch's relative acceptance (RA) index does not actually measure nations' preferences for transactions with one another. Using a modified measure and 1928–71 data for international merchandise trade, I conclude (1) that EEC members' preferences for one another have increased only modestly since the establishment of their Common Market; and (2) that other groups of Western industrial countries have shown a greater rise in intragroup trade preferences in the same period than the EEC. There follows a discussion on the relationship between intraregional transactions preferences and regional political integration. Two conclusions are reached: (1) high intraregional transactions saliences are necessary but not sufficient preconditions for political integration; and (2) rising intraregional transactions preferences must follow political integration. Trade data suggest that, for the EEC, intraregional saliences are probably high enough to permit integration; but slowly increasing preferences suggest that only a little integration can actually have occurred.
Using an Interactive Singing Software Program: A Comparative Study of Struggling Middle School Readers

Software that teaches users to sing in tune and in rhythm while providing real-time pitch tracking was used in a study of struggling middle school readers. The software, Carry-a-Tune (CAT) was originally developed to improve singing; however, since it involves a repeated reading format, we used it to determine its effect on comprehension and reading achievement. Twenty-four students in grades 7 and 8 utilized the software program for 30 minutes, three times a week for 9 weeks. A matched control group of 24 students had a different reading experience during the same time period. The mean pretest instructional reading level for both groups was fourth grade. The mean instructional level scores for the treatment group improved significantly (7 months during the 9-week study). The matched control group students did not experience gains. Sustainability data from assessment 4 months after the study's conclusion indicated treatment students gained another 6 months. This placed them solidly in mid-fifth grade for ...
Treatment of Obstructive Sleep Apnea in Pediatric Patients Behavioral Intervention for Compliance With Nasal Continuous Positive Airway Pressure

This study evaluated the efficacy of behavioral techniques (i.e., parent training, modeling, and desensitization) to facilitate use of nasal continuous positive airway pressure (CPAP) in four children with obstructive sleep apnea (OSA) secondary to anatomic disorder of the upper airway. All patients tolerated CPAP with training: Polysomnographic data revealed improvement in sleep architecture, apnea, and oxygenation, and patients were discharged on CPAP units. All patients continued to use CPAP throughout the 3-month follow-up period and none required additional treatment for OSA. Three of four patients continued to use CPAP at the 9-month follow-up visit. Treatment resulted in improvements in alertness, attention/concentration, and behavior/temperament. Children generally have been considered poor candidates for nasal CPAP, and historically they have been offered instead more invasive procedures. This study suggests that CPAP is a viable treatment for such children when paired with behavioral interventions that facilitate its use.
Quadriceps muscle function after exercise in men and women with a history of anterior cruciate ligament reconstruction

Context: Sex differences in lower extremity neuromuscular function have been reported after anterior cruciate ligament reconstruction (ACLR). Research evidence supports different levels of fatigability in men and women and between patients with ACLR and healthy controls. The influence of sex on the response to continuous exercise in patients with ACLR is not clear. Objective: To compare quadriceps neuromuscular function after exercise between men and women with ACLR. Design: Descriptive laboratory study. Setting: Laboratory. Patients or Other Participants: Twenty-six active volunteers (13 men [50%]: age = 24.1 ± 4.4 years, height = 179.1 ± 9.8 cm, mass = 80.1 ± 9.4 kg, months since surgery = 43.5 ± 37.0; 13 women [50%]: age = 24.2 ± 5.6 years, height = 163.0 ± 5.9 cm, mass = 62.3 ± 8.3 kg, months since surgery = 45.8 ± 42.7) with a history of unilateral primary ACLR at least 6 months earlier. Intervention(s): Thirty minutes of continuous exercise comprising 5 separate 6-minute cycles, including 5 minutes ...
Leber Congenital Amaurosis Caused by a Homozygous Mutation (R90W) in the Homeodomain of the Retinal Transcription Factor CRX: Direct Evidence for the Involvement of CRX in the Development of Photoreceptor Function

The CRX (cone-rod homeobox) gene is specifically expressed in developing and mature photoreceptors and encodes an otd/Otx-like paired homeodomain protein. Mutant alleles of the CRX gene have recently been associated with autosomal dominant cone-rod dystrophy (CORD) as well as dominant Leber congenital amaurosis (LCA). Since LCA is more commonly inherited in an autosomal recessive manner, we examined a cohort of recessive LCA patients for CRX mutations. A homozygous substitution of arginine (R) at codon 90 by tryptophan (W) was identified in the CRX homeodomain of one of the probands who was nearly blind from birth. A group of 48 control individuals and 190 previously characterized CORD probands did not reveal this sequence change. The mutant CRX R90W homeodomain demonstrated decreased binding to the previously identified cis sequence elements in the rhodopsin promoter. In transient transfection experiments, the mutant protein showed significantly reduced ability to transactivate the rhodopsin promoter, as well as lower synergistic activation with the bZIP transcription factor NRL. Heterozygosity of the mutant CRX (R90W) allele was detected in both parents and in an older sibling. Ophthalmologic examination and electroretinography revealed a subtle abnormality of cone function in both the parents. These data suggest that the R90W mutation results in a CRX protein with reduced DNA binding and transcriptional regulatory activity and that the subsequent changes in photoreceptor gene expression lead to the very early onset severe visual impairment in LCA.
Glycation and microglial reaction in lesions of Alzheimer's disease

Single, double, and triple immunostaining of cryostat sections of elderly normal and Alzheimer disease (AD) brain was performed with monoclonal and polyclonal antibodies to advanced glycation end products (AGE). The sections were counterstained with thioflavin-S or with immunocytochemistry for Aβ and also stained with markers for microglia. AGE-immunoreactivity was detected in senile plaques and neurofibrillary tangles (NFT). AGE immunoreactivity was most intense in dense or reticular amyloid deposits and extracellular NFT, while intracellular NFT and diffuse amyloid had less AGE immunoreactivity. This pattern of immunoreactivity was similar to that noted in previous studies with antibodies to apolipoprotein-E (apo-E). Therefore, double labeling with antibodies to apo-E and AGE was performed. AGE immunoreactivity colocalized to a very high degree with apo-E immunoreactivity, except that relatively more intense apo-E immunoreactivity was detected in amyloid deposits and more intense AGE immunoreactivity in NFT. The lesions that were immunostained with antibodies to AGE and apo-E were often, but not always, associated with a local microglial reaction. The results raise the possibility that apo-E or a fragment of apo-E may be glycated. Biochemical studies are needed to determine the extent of possible apo-E glycation in AD. The present results raise the possibility that glycation may serve as one of the signals for activation of microglia associated with amyloid deposits and extracellular NFT.
Nonunion with Extensive Bone Loss: Reconstruction with Ilizarov Techniques and Orthobiologics

Numerous procedures for the treatment of chronic bone loss have been devised to reconstitute bone stock, obtain union, and provide a stable functional limb. These procedures include bone transport as well as new orthobiologic adjuvant methodologies. Bone transport is a reliable technique; however, it is very time consuming, requires extreme patient compliance, and requires diligence on part of the surgeon to avoid potential complications. With advancements in external fixator technology, newer frame configurations have simplified the mechanics of frame mounting and transport. New frames permit constant adjustment of the proposed docking site without the misalignment potential that can occur with traditional circular frame constructs. Development of hydroxy–appetite-coated pins and other substrate biomaterials, as well as advancements in intramedullary designs, have decreased the time period requiring external transport devices. The emergence of orthobiologics holds great promise for large skeletal defects. The ability to augment large regenerate segments with percutaneously applied growth factor adjuvants to reduce prolonged consolidation times in patients is an attractive alternative a patient spending 1.5 to 2 years in an external transport device. New composite grafting techniques have been devised to be applied in a staged fashion after the development of a well-vascularized psuedomembrane in the defect tract. These techniques include composite grafting using reamer irrigator aspirator techniques, demineralized bone matrix and cellular marrow concentrates, bone morphogenetic protein with allograft composites, and the implantation of titanium cages directly into the defect sites augmented with all the aforementioned adjuvants. This article reviews the current state of defect management.
Mesoscale modeling of refractive conditions during the VOCAR experiment

A mesoscale model was run in a data assimilation cycle throughout the 12-day period of the Variability of Coastal Atmospheric Refractivity (VOCAR) experiments's Intensive Observing Period (IOP). A developing synoptic low, a mesoscale eddy, sea-land breezes, mountain-valley winds, and coastal low-level jets (LLJs) are some of the phenomena modeled, and to some extent, observed during VOCAR. Impacts of these processes on the marine atmospheric boundary layer (ABL) and microwave refractivity are highlighted. >
Monitoring Grape Berry Moth (Paralobesia viteana: Lepidoptera) in Commercial Vineyards using a Host Plant Based Synthetic Lure

For some Lepidopteran pests, such as the grape berry moth Paralobesia viteana (Clemens), poor correlation between males captured in traps baited with sex pheromone and oviposition activities of female moths has called into question the value of pheromone-based monitoring for these species. As an alternative, we compared the capture of female and male grape berry moth in panel traps baited with synthetic host volatiles with captures of males in pheromone-baited wing traps over two growing seasons in two blocks of grapes in a commercial vineyard in central New York. Lures formulated in hexane to release either 7-component or 13-component host volatile blends captured significantly more male and female grape berry moth on panel traps compared with the numbers captured on panel traps with hexane-only lures. For both sexes over both years, the same or more moths were captured in panel traps along the forest edge compared with the vineyard edge early in the season but this pattern was reversed by mid-season. Male moths captured in pheromone-baited wing traps also displayed this temporal shift in location. There was a significant positive correlation between captured males and females on panel traps although not between females captured on panel traps and males captured in pheromone-baited traps for both years suggesting pheromone traps do not accurately reflect either female or male activity. Male moths captured in pheromone traps indicated a large peak early in each season corresponding to first flight followed by lower and variable numbers that did not clearly indicate second and third flights. Panel trap data, combining males and females, indicated three distinct flights, with some overlap between the second and third flights. Peak numbers of moths captured on panel traps matched well with predictions of a temperature-based phenology model, especially in 2008. Although effective, panel traps baited with synthetic host lures were time consuming to deploy and maintain and captured relatively few moths making them impractical, in the current design, for commercial purposes.
B-lymphoblastic transformation of mantle cell lymphoma/leukemia with “double hit” changes

Mantle cell lymphoma is a mature B-cell neoplasm composed of small to medium-sized atypical lymphocytes and has a characteristic t(11;14)(q13;q32) translocation, with a variably aggressive and overall incurable course. More aggressive histologic variants have been described, as well as rare cases of transformation to other large cell lymphomas. Here, we describe a novel case of large cell blastic transformation of mantle cell lymphoma/leukemia at presentation with unusual immunophenotypic and cytogenetic features, most consistent with B-lymphoblastic leukemia. Morphologic findings include sheets of large blasts replacing the bone marrow, as well as occasional small to medium-sized atypical lymphocytes in the background. The blasts express CD19, PAX5, CD10, Cyclin D1, and TdT but are negative for CD5, CD20, and BCL2 by immunophenotyping. Cytogenetic studies show a complex karyotype with t(11;14), monosomy 13, gains of 8q, and MYC gene rearrangement and amplification among other changes. This unique case of blastic TdT-positive B-cell leukemia arising from mantle cell lymphoma may represent transformation with complex cytogenetic abnormalities including “double hit” changes. This distinctive presentation may expand our understanding of the biology behind mantle cell lymphoma progression.
VH3. Technical Aspects of Intracranial-Extracranial (EC-IC) Bypass: Resurrection of a Nearly Extinct Operation

Background: Open abdominal aortic aneurysm repair has become increasingly less common in the endovascular era. This approach to open aortic aneurysm repair illustrates the usefulness of mobilizing the right colon cranially to aid in exposing the aorta. This approach is particularly helpful in cases of prior left hemicolectomy or in cases that require suprarenal clamping. Technical Description: After a midline laparotomy incision is performed, the cecum and right colon are mobilized along an avascular plane to allow for reflection of the right colon cranially. The duodenum is mobilized to further expose the aorta. The cecum, right colon, and small bowel is packed towards the right upper quadrant to allow for optimal exposure of the aorta. Aortic aneurysm repair is performed in standard fashion. The cecum is returned to the right lower quadrant and the small bowel is returned to its native location and covered with omentum prior to abdominal wall closure.
Plasmalogens, phospholipases A2 and signal transduction

Several lines of evidence indicate that the breakdown of plasmalogens in neural membranes during neurodegenerative diseases is a receptor-mediated process catalyzed by a plasmalogen-selective phospholipase A2. This enzyme has recently been purified from bovine brain. It does not require Ca2+ and is localized in cytosol. It has a molecular mass of 39 kDa and is strongly inhibited by glycosaminoglycans, with the pattern of inhibition being heparan sulfate0 > hyaluronic acid > chondroitin sulfate > heparin. This plasmalogen-selective phospholipase A2 is also inhibited by gangliosides and sialoglycoproteins. Substrate specificity and the effects of metal ions, detergents and inhibitors suggest that this phospholipase A2 is different from the well-known 85 kDa Ca2+-dependent cytosolic phospholipase A2 that has recently been cloned and is not plasmalogen-selective. The plasmalogen-selective phospholipase A2 may be regulated by glycosaminoglycans and sialoglycoconjugates and may be involved in the regulation of K+ channels. This enzyme, which plays a major role in the release of fatty acids during ischemic injury and reperfusion, shows promise as a major target for drug therapy.
Rescuing Children from the Marriage Movement: The Case Against Marital Status Discrimination in Adoption and Assisted Reproduction

Much of the current groundswell of support for heterosexual-only marriage in the United States arises from the belief that children do best when raised by their married, biological parents. This sense of what marriage and biological ties mean to children individually and to society as a whole has led states to pass laws that directly or indirectly bar unmarried persons from becoming parents through adoption or assisted reproduction, contexts in which parent-child relationships often lack any biological component. Upon close examination, discrimination against the unmarried in adoption and assisted reproduction relates neither to the purposes of marriage nor to child welfare. In the context of assisted reproduction, marital-status discrimination fails to survive interpretivist scrutiny, a standard for policymaking requiring legislation to conform not only to constitutional strictures but also to contemporary legal principles and legislative trends. Marital-status discrimination in adoption, apparent in the law's differential treatment of step-parent adoption and second-parent adoption, fails to meet interpretivism's requirement that the law exhibit both neutrality and consistency. Only by satisfying an interpretivist standard can discrimination against the unmarried in assisted reproduction and adoption command broad public support - the essence of all sound public policy. By continuing to advocate vociferously for favored treatment of married couples in matters of legal parenthood, the heterosexuals-only marriage movement not only works against our legal traditions and values, but also ultimately undermines the welfare of many children whose best hope lies with parents the law does not allow to marry.
Abstract 2866: Defining epigenetic vulnerabilities in synovial sarcoma

Synovial sarcoma constitutes 10% of all soft-tissue sarcomas and arises most frequently in adolescents and young adults. The defining genetic event of synovial sarcoma and main driver of the disease is the translocation of the SS18 gene on chromosome 18q11 to either the SSX1 and SSX2 genes located on chromosome Xp11. The resulting SS18-SSX fusion oncogene lacks a DNA binding domain, but is thought to exert its function via interaction with transcription factors and chromatin remodelers such as polycomb-group chromatin remodeling factors, and components of the SWI/SNF complex. The fact that the fusion oncogene is the defining event in this disease suggests that, on its own, it is able to generate an epigenetic profile that drives tumorigenesis. In this study we expressed SS18-SSX2 in C2C12 myoblasts to recreate the epigenetic events driving synovial sarcoma. C2C12 myoblasts expressing SS18-SSX1/2 did not show significant differences in cell growth however became completely refractory to differentiation to myotubes. In addition, knockdown of SS18-SSX2 in a mouse synovial sarcoma cell line (derived from a mouse model in which the human SS18-SSX2 fusion oncogene is expressed in the myogenic progenitor compartment) led to strong growth arrest and induction of induction of p16 and p21 cell cycle regulators. This results support the notion that the SS18-SSX oncogene drives tumorigenesis by blocking differentiation programs and by repressing tumor suppressor genes to maintain self-renewal of synovial sarcoma cells. To identify epigenetic vulnerabilities that are specifically generated by the SS18-SSX fusion protein we screened two cell lines using an shRNA library targeting epigenetic modulators: the synovial sarcoma cell line mentioned above and C2C12 myoblasts. Three control shRNAs targeting the SS18-SSX2 oncogene were within the top depletion hits in the synovial sarcoma cell line but were neutral in the C2C12 myoblasts, validating the screen performance. To uncover SS18-SSX specific hits we concentrated in genes within this list that specifically depleted in the synovial sarcoma cell line but not in myoblasts. Genes within this list and to which at least two independent shRNAs scored were subjected to extensive one-by one validation. Our results may uncover epigenetic mechanisms required to maintain self-renewal in synovial sarcoma. Citation Format: Ana Banito, Nilgun Tasdemir, Marc Ladanyi, Scott W. Lowe. Defining epigenetic vulnerabilities in synovial sarcoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2866. doi:10.1158/1538-7445.AM2015-2866
Multimodality Intravascular Imaging to Evaluate Sex Differences in Plaque Morphology in Stable CAD

Abstract Objectives The aim of this study was to evaluate sex differences in plaque morphology in stable coronary artery disease (CAD) patients using a multimodality intravascular imaging approach. Background Differences in atherosclerotic burden and plaque morphology between men and women is a focus of treatment and preventative measures. Methods We retrospectively analyzed data from 383 patients with stable CAD who were referred for angiography and underwent optical coherence tomography. Among them, 128 also underwent intravascular ultrasound (IVUS)/near infrared spectroscopy. Results Of the 383 patients included in the study, 268 were men and 115 were women. Women tended to be older (66 ± 10 years of age vs. 62 ± 11 years of age; p = 0.002) and have more comorbidities including hypertension (97% vs. 90%; p = 0.031), diabetes with insulin use (18% vs. 10%; p = 0.043), obesity (body mass index 30 kg/m2 vs. 28 kg/m2; p = 0.022), and lower estimated glomerular filtration rate (88 ml/min/1.73m2 vs. 98 ml/min/1.73m2; p = 0.001). Optical coherence tomography data demonstrated that there was no sex difference in plaque morphology as characterized by maximum lipid arc, lipid length, lipid volume index, minimum cap thickness, incidence of thin cap fibroatheroma, microvessels, macrophages, and calcification. There was also no difference in maximal lipid core burden index at the 4-mm maximal segment as seen on near infrared spectroscopy. Plaque characteristics by IVUS were similar between men and women except for an increase in plaque burden in men compared to women in the reference segment (44.4 vs. 39.3; p = 0.031). After adjusting for age, body mass index, percutaneous coronary intervention history, and clinical risk factors, sex was not found to be an independent predictor of severe plaque burden by IVUS. Conclusion Among men and women with stable CAD referred for coronary angiography, there was no difference in plaque characteristics as assessed by multimodality imaging. These findings, which are hypothesis generating, suggest that equally aggressive primary and secondary preventive efforts irrespective of sex must be undertaken.
Impact of the Reputation Quotient® on Investment Performance

Reputation Quotients (RQs®) produced by Harris Interactive, Inc. are a presumed credible measure of corporate reputation that assesses corporate reputations employing six drivers, which are correlated with 20 attributes. Reputations appear to be an important characteristic of a firm, which transcends a company’s current production and financial statements to set a path for future performance. Although many years and multiple factors go into creating a reputation, this study found that past share price performance was unrelated to company reputation. However, reputation does appear to provide insight into future firm performance. Firms with the worst reputations often seem to have trouble providing a return sufficient to cover risk, especially in the absence of dividends. By comparison, firms with the best reputations tend to have lower risk, whether measured in terms of systematic risk or total risk, and therefore generate significantly higher risk-adjusted rates of return.
Perturbations of peptide-induced lateral phase separations in phosphatidic acid bilayers by the inhalation anesthetic methoxyflurane.

The effect of methoxyflurane in a clinical concentration range on a phospholipid-peptide interaction in model membranes was studied by electron paramagnetic resonance. Thermotropic phase transition curves of negatively charged phosphatidic acid bilayers in the presence of the peptide antibiotic polymyxin-B were obtained using the spin probe 2,2,6,6-tetramethylpiperidine-1-oxyl. Polymyxin interacts strongly with phosphatidic acid membranes, causing lateral phase separations. Domains of peptide-bound phospholipids are formed in a matrix of a bilayer of unbound phosphatidic acid. The phase transition of the polymyxin-phosphatidic acid domain is decreased by about 13° as compared with a pure phosphatidic acid bilayer. The phosphatidic acid matrix surrounding these domains exhibits a somewhat broadened and lowered phase transition due to the presence of some monomeric polymyxin. Addition of the inhalation anesthetic methoxyflurane progressively disrupts the polymyxin-induced lateral phase separation, leading to a homogeneously dispersed phase at concentrations above 100 mmoles of anesthetic per mole of lipid. Application of high pressure antagonizes the effect of the anesthetic on the phase transition temperature of the free phosphatidic acid matrix and antagonizes the disruption of the phosphatidic acid-polymyxin domain. In a phosphatidic acid bilayer containing polymyxin, 4 moles %, a pressure of 100 atmos absolute (ATA) antagonizes the effect of 30 mmoles of methoxyflurane per mole of lipid. The latter concentration is equal to that produced in nerve membranes during clinical anesthesia, while a pressure of 100 ATA is sufficient to reverse anesthesia in mice and tadpoles. A much larger antagonism of the pressure and inhalation anesthetic effects is observed in the phase transition temperature of the surrounding phosphatidic acid phase than in the polymyxin-phosphatidic acid domains. However, at methoxyflurane concentrations greater than 100 mmoles/mole of lipid, when the polymyxin-phosphatidic acid domains are completely dispersed and form a homogeneous bilayer structure, the effect of pressure is only 20% of that observed in a pure phosphatidic acid vesicle containing the same concentration of methoxyflurane.
Not just plain vanilla DNA nanotechnology: other pairings, other backbones

Up to this point, we have been talking largely about Watson–Crick double helical DNA. No variations in the base-pairing and no variations in the backbone. Here we are going to discuss just a little bit of the work that is going on with other DNA structures, work that entails non-DNA backbones, and other species organized by DNA nanoconstructs. This chapter is not meant to be a comprehensive review of variations on the theme of either DNA nor its interactions with other species, just a taste to stimulate the reader to pursue other materials on her own. Paukstelis DNA structure. Perhaps the first place to start is DNA, but DNA that is not simply Watson–Crick. A robust motif discovered in a single-crystal structure is shown in Figure 13-1. This motif contains three conventional nucleotide pairs and three parallel pairs, consisting of one A–G pair and two G–G pairs. This overall motif is shown in stereo in Figure 13-2. A salient feature of the structure is that it crystallizes in a hexagonal space group with a cavity whose volume is 300 A 3 , which is shown in stereo in Figure 13-3a. The robustness of the motif is demonstrated by the fact that the Watson–Crick portion of the motif can be extended by 10 nucleotide pairs, yet the space group remains the same. Although the resolution of the crystal decreases somewhat, the cavity is greatly expanded by this expansion, so its volume is now increased markedly, as shown in Figure 13-3b. Triplex DNA. In addition to the simple double helical motif, there are other helical motifs that have been characterized. The earliest of these was the DNA triplex, wherein a pyrimidine–purine–pyrimidine structure was formed (see Figures 2-4 and 2-5). There are a number of utilities that one can imagine for such systems in DNA constructs. Without disrupting the double helix, it is possible to address specifically designed locations within the assembly by adding a triplex-forming oligonucleotide (TFO). One could imagine tethering both small molecules and macromolecules to DNA constructs by the use of triplex associations. An example of triplex DNA added to DNA tensegrity-triangle crystals (see Chapter 7, especially Figure 7-23) is shown schematically in Figure 13-4; crystals to which triplex molecules containing dyes have been attached are shown in Figure 13-5.
The Contest Problem Book VIII: American Mathematics Competitions (AMC 10), 2000-2007 Contests

In the year 2000, the Mathematical Association of America initiated the American Mathematics Competitions 10 (AMC 10) for students up to grade 10. The Contest Problem Book VIII is the first collection of problems from that competition covering the years 2001-2007. J. Douglas Faires and David Wells were the joint directors of the AMC 10 and AMC 12 during that period, and have assembled this book of problems and solutions. There are 350 problems from the first 14 contests included in this collection. A Problem Index at the back of the book classifies the problems into the following major subject areas: Algebra and Arithmetic, Sequences and Series, Triangle Geometry, Circle Geometry, Quadrilateral Geometry, Polygon Geometry, Counting Coordinate Geometry, Solid Geometry, Discrete Probability, Statistics, Number Theory, and Logic. The major subject areas are then broken down into subcategories for ease of reference. The Problems are cross-referenced when they represent several subject areas.
Trends in Thermoresponsive Behavior of Lipophilic Polymers

In an effort to find correlations between size changes with temperature of lipophilic polymers in solution and viscosity index trends, the determination of the size of thermoresponsive polymers of various architectures (linear, comb-like, star, and hyperbranched) using two experimental techniques under infinite dilution conditions (0.5% w/w) – dynamic light scattering and small angle neutron scattering, and predictive molecular dynamics simulations is described herein. Viscosity index is an important parameter for lubricants and other rheological applications. The aim of this work was to predict polymer behavior as viscosity index improvers (VIIs) using tools which require minimal amounts of material, as opposed to measuring kinematic viscosities, which require multigram quantities. There were no significant correlations between changes in polymer size with temperature and viscosity index (VI). The polymers with the highest VI (polyalkyl methacrylate - PAMA and Star PAMA) had polar backbones in contrast t...
Women In The United States Experience High Rates Of Coverage ‘Churn’ In Months Before And After Childbirth

Insurance transitions—sometimes referred to as “churn”—before and after childbirth can adversely affect the continuity and quality of care. Yet little is known about coverage patterns and changes for women giving birth in the United States. Using nationally representative survey data for the period 2005–13, we found high rates of insurance transitions before and after delivery. Half of women who were uninsured nine months before delivery had acquired Medicaid or CHIP coverage by the month of delivery, but 55 percent of women with that coverage at delivery experienced a coverage gap in the ensuing six months. Risk factors associated with insurance loss after delivery include not speaking English at home, being unmarried, having Medicaid or CHIP coverage at delivery, living in the South, and having a family income of 100–185 percent of the poverty level. To minimize the adverse effects of coverage disruptions, states should consider policies that promote the continuity of coverage for childbearing women, pa...
Nursing home admission risk and the cost-effectiveness of community-based long-term care: a framework for analysis.

Abstract The relationship of prior risk of nursing home entry among applicants for community-based long-term care (CB/LTC) services to cost-effective admission decisions is investigated using decision analytic techniques. It is shown that using such evaluation criteria as have predominated in the major CB/LTC demonstrations, the necessary minimum level of prior risk is well above that typical of those actually enrolled. It is further shown that the remedy usually proposed, increasing the rigor and accuracy of enrollment screening, is unlikely to be of much practical effect. A case can be made, however, for defining the benefits of CB/LTC more broadly, in which case it may become cost-effective to enroll lower-risk applicants.
Biology of IL‐38 and its role in disease

IL-38 belongs to the IL-36 cytokines, which in turn are part of the IL-1 family. The first biological function of IL-38 described was blocking the activation of the IL-36R signaling similar to IL-36Ra. Since IL-36 cytokines require processing in order to become fully active, it is likely that IL-38 also must be processed to become maximally active. However, the protease(s) responsible for this is currently not known. In addition of IL-38 binding IL-36R, it has been proposed it can also interact with the co-receptor TIGIRR2. IL-38 is expressed in several tissues including tonsils, placenta, heart and brain, and IL-38 has been implicated in a wide variety of diseases including cardiovascular and autoimmune disease. Here, we discuss the discovery and biological function of IL-38, and its role in the pathogenesis of a wide variety of diseases.
Laparoscopy-Assisted Appendectomy via the patent umbilical ring (Umbilical hernia): A Case Report

Umbilical hernia aswell as acute appendicitis are two of the most common problems seen by paediatric surgeons, although rarely simultaneously. When detected the operative approach is adjusted. We perform the a laparoscopically assisted appendectomy trough through the an excised umbilical hernia sac opening. The operative technique is presented. The most important advantages are single general anesthesia for the two surgical procedures and the use of present openingpatent umbilical ring as an access to inflamed appendix, what is the essence of a minimally invasive surgery,. Evaluating the results of the appendectomy superior cosmetic end result, minimal scaring and lower stress index are the advantages in comparisoncompared to the conventional open surgery. Shorter procedure and reduced costs are the advantages in comparison to the three port laparoscopic appendectomy. Efficacy and safety are the same as in single umbilical hernia repair. Keywords : Umbilical hernia, appendicitis, laparoscopically assisted appendectomy. African Journal of Paediatric Surgery Vol. 4 (1) 2007: pp. 51-54
MRI and DW-MRI of Acute Pyelonephritis (APN)

An accurate evaluation of acute pyelonephritis (APN) requires imaging of parenchymal involvement. When no predisposing conditions to complicated APN are found at US, noncomplicated APN is suspected, and CT or MRI should be performed. As patients with noncomplicated APN are mostly young women, gadolinium-enhanced (GE) MRI is preferred. Diffusion-weighted (DW) MRI might be quicker and cheaper than standard GE-MRI and is reliable for diagnosing or ruling out noncomplicated APN, due to the high diagnostic agreement with GE-MRI. However, GE-MRI is still mandatory for accurately staging APN within 48 h after diagnosis. DWI with ADC evaluation might be also useful in following therapeutic management of APN, without using ionizing radiation or contrast media.
Investing in each other--Balint groups and the patient-doctor relationship.

Balint groups, discussion groups for medical students to reflect on their relationships with patients, are an effective way of investing in the patient-physician relationship.
Emergence of a New Perspective

Winston Churchill once remarked, “First we shape our buildings and afterwards our buildings shape us.” Churchill was incorrect. Not because people are unaffected by the physical contexts within which they reside; a growing scientific literature affirms, in fact, that they are. Rather Churchill’s comment is misleading, for in its compelling simplicity there is implicit an assumption that the effect of environment on behavior is direct, passive, simple, and readily predictable. Nothing could be further from the truth.
Deciphering splenic marginal zone lymphoma pathogenesis: the proposed role of microRNA

Splenic marginal zone lymphoma (SMZL) is a malignancy of mature B-cells that primarily involves the spleen, but can affect peripheral organs as well. Even though SMZL is overall considered an indolent malignancy, the majority of cases will eventually progress to be more aggressive. In recent years, the gene expression profile of SMZL has been characterized in an effort to identify: 1) the etiology of SMZL, 2) biological consequences of SMZL, and 3) putative therapeutic targets. However, due to the vast heterogeneity of the malignancy, no conclusive target(s) have been deciphered. However, the role of miRNA in SMZL, much as it has in chronic lymphocytic leukemia, may serve as a guiding light. As a result, we review the comprehensive expression profiling in SMZL to-date, as well as describe the miRNA (and potential mechanistic roles) that may play a role in SMZL transformation, particularly within the 7q region.