cssi/SciSciGPT-SciSciNet huggingface dataset:
Reauthorize, Revise, and Remember: Refocusing the No Child Left Behind Act To Fulfill Brown's Promise

The adoption of the No Child Left Behind Act of 2001 (NCLB) 1 was billed as a watershed moment in education policy. 2 Yet, NCLB did not mark the federal government's first major foray into education policy; in fact, it was just the most recent incarnation of the Elementary and Secondary Education Act of 1965 (ESEA). 3 Enacted at the height of the civil rights movement and as part of America's “War on Poverty,” the ESEA is a federal civil rights statute at its core, designed to level the playing field and expand educational opportunity for poor children and children of color. 4 *170 While it was ostensibly designed to continue the ESEA's legacy of advancing equitable educational opportunities, 5 NCLB has been treated in its implementation more as a vehicle for a particular approach to “education reform” than as a means to further civil rights principles such as inclusion and equal opportunity. 6
Biophysical prediction of protein–peptide interactions and signaling networks using machine learning

In mammalian cells, much of signal transduction is mediated by weak protein-protein interactions between globular peptide-binding domains (PBDs) and unstructured peptidic motifs in partner proteins. The number and diversity of these PBDs (over 1,800 are known), their low binding affinities and the sensitivity of binding properties to minor sequence variation represent a substantial challenge to experimental and computational analysis of PBD specificity and the networks PBDs create. Here, we introduce a bespoke machine-learning approach, hierarchical statistical mechanical modeling (HSM), capable of accurately predicting the affinities of PBD-peptide interactions across multiple protein families. By synthesizing biophysical priors within a modern machine-learning framework, HSM outperforms existing computational methods and high-throughput experimental assays. HSM models are interpretable in familiar biophysical terms at three spatial scales: the energetics of protein-peptide binding, the multidentate organization of protein-protein interactions and the global architecture of signaling networks.
Augmenting the Pressure-Based Pasteurization of Listeria monocytogenes by Synergism with Nisin and Mild Heat

The current study investigated Listeria monocytogenes inactivation using mild heat with elevated hydrostatic pressure and nisin under buffered condition. A four-strain pathogen mixture was exposed to 0 (control) and up to 9 min of (1) 4 °C elevated pressure; (2) 4 °C elevated pressure and nisin; (3) 4 °C nisin; (4) heat at 40 °C; (5) 40 °C elevated pressure; (6) 40 °C elevated pressure and nisin; and (7) 40 °C nisin. Elevated hydrostatic pressure at 400 MPa (Hub880 Explorer, Pressure BioScience Inc., Easton, MA, USA) and nisin concentration of 5000 IU/mL were used in the trials. Analyses of variance were conducted, followed by Dunnett’s- and Tukey-adjusted means separations. Under conditions of these experiments, nisin augmented (p < 0.05) decontamination efficacy of 40 °C heat and elevated hydrostatic pressure treatments, particularly at treatment interval of 3 min. This synergism with nisin faded away (p ≥ 0.05) as the treatment time for thermal, high-pressure, and thermal-assisted pressure processing increased. The results of our study, thus, exhibit that practitioners and stakeholders of pressure-based technologies could benefit from synergism of mild heat and nisin for short-term, high-pressure pasteurization treatments to achieve microbial safety and economic feasibility comparable to traditional heat-treated products.
Bisphenols as Environmental Triggers of Thyroid Dysfunction: Clues and Evidence

Bisphenols (BPs), and especially bisphenol A (BPA), are known endocrine disruptors (EDCs), capable of interfering with estrogen and androgen activities, as well as being suspected of other health outcomes. Given the crucial role of thyroid hormones and the increasing incidence of thyroid carcinoma in the last few decades, this review analyzes the effects of BPS on the thyroid, considering original research in vitro, in vivo, and in humans published from January 2000 to October 2019. Both in vitro and in vivo studies reported the ability of BPs to disrupt thyroid function through multiple mechanisms. The antagonism with thyroid receptors (TRs), which affects TR-mediated transcriptional activity, the direct action of BPs on gene expression at the thyroid and the pituitary level, the competitive binding with thyroid transport proteins, and the induction of toxicity in several cell lines are likely the main mechanisms leading to thyroid dysfunction. In humans, results are more contradictory, though some evidence suggests the potential of BPs in increasing the risk of thyroid nodules. A standardized methodology in toxicological studies and prospective epidemiological studies with individual exposure assessments are warranted to evaluate the pathophysiology resulting in the damage and to establish the temporal relationship between markers of exposure and long-term effects.
A Study of the Fundamental Performance Characteristics of GPUs and CPUs for Database Analytics

There has been significant amount of excitement and recent work on GPU-based database systems. Previous work has claimed that these systems can perform orders of magnitude better than CPU-based database systems on analytical workloads such as those found in decision support and business intelligence applications. A hardware expert would view these claims with suspicion. Given the general notion that database operators are memory-bandwidth bound, one would expect the maximum gain to be roughly equal to the ratio of the memory bandwidth of GPU to that of CPU. In this paper, we adopt a model-based approach to understand when and why the performance gains of running queries on GPUs vs on CPUs vary from the bandwidth ratio (which is roughly 16× on modern hardware). We propose Crystal, a library of parallel routines that can be combined together to run full SQL queries on a GPU with minimal materialization overhead. We implement individual query operators to show that while the speedups for selection, projection, and sorts are near the bandwidth ratio, joins achieve less speedup due to differences in hardware capabilities. Interestingly, we show on a popular analytical workload that full query performance gain from running on GPU exceeds the bandwidth ratio despite individual operators having speedup less than bandwidth ratio, as a result of limitations of vectorizing chained operators on CPUs, resulting in a 25× speedup for GPUs over CPUs on the benchmark.
NMR Studies of Retroviral Genome Packaging

Nearly all retroviruses selectively package two copies of their unspliced RNA genomes from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs. Over the past four decades, combinations of genetic experiments, phylogenetic analyses, nucleotide accessibility mapping, in silico RNA structure predictions, and biophysical experiments were employed to understand how retroviral genomes are selected for packaging. Genetic studies provided early clues regarding the protein and RNA elements required for packaging, and nucleotide accessibility mapping experiments provided insights into the secondary structures of functionally important elements in the genome. Three-dimensional structural determinants of packaging were primarily derived by nuclear magnetic resonance (NMR) spectroscopy. A key advantage of NMR, relative to other methods for determining biomolecular structure (such as X-ray crystallography), is that it is well suited for studies of conformationally dynamic and heterogeneous systems—a hallmark of the retrovirus packaging machinery. Here, we review advances in understanding of the structures, dynamics, and interactions of the proteins and RNA elements involved in retroviral genome selection and packaging that are facilitated by NMR.
Delayed Diagnosis of Fibrocartilaginous Embolism: Assessing the Vertebral Body on MRI (P4.3-008)

Objective: Fibrocartilaginous embolism (FCE) is a well described phenomena that makes up 5.5% of spinal cord infarcts. It refers to the migration of fibrocartilaginous nucleus pulposus material from the vertebral body through nearby vasculature and embolizes into one of the spinal cord vessels. The embolic event may not follow the typical vascular distribution seen in a majority of spinal cord infarcts and could be frequently misdiagnosed on neuroimaging review. Background: A 43 year old healthy man presented as a transfer from an outside hospital after acute onset of bilateral lower extremity weakness and subsequent spasticity. Outside hospital MRI spine was initially interpreted as without cord signal abnormality, compression or enhancement. At our institution on review of the same imaging, we found a possible subtle cord T2 hyper-intensity in the left posterolateral cord at the T10–11 level concerning for demyelination, possibly transverse myelitis. The patient was initiated on high-dose corticosteroids however the patient did not show clinical improvement. Therefore, MRI spine was repeated one week later with dedicated Diffusion Weighted Imaging (DWI). There was not only a more definitive T2 hyperintense spinal cord lesion but also corresponding mild diffusion-restriction in the cord. Additionally, there was T11 vertebral body infarction which is a rare but diagnostic feature essential in distinguishing FCE from an inflammatory cord lesion. Design/Methods: N/A Results: N/A Conclusions: This case was originally misdiagnosed as idiopathic transverse myelitis but did not respond appropriately to management. The MRI finding of vertebral body infarction accompanying the spinal cord signal abnormality is a rare but highly specific finding for FCE proposed to be in the same arterial distribution. If found radiographically, vertebral body infarction can aid in timely proper diagnosis, avoidance of unnecessary testing such as cerebrospinal fluid analysis and excess therapeutic exposure such as high-dose corticosteroids. Disclosure: Dr. Isaac has nothing to disclose. Dr. Swavely has nothing to disclose. Dr. Talekar has nothing to disclose. Dr. McCall has nothing to disclose.
Inverse methods for consistent quantification of seafloor anoxia using uranium isotope data from marine sediments

Abstract Uranium isotopes ( δ 238 U) have quickly become one of the most widely-used redox proxies in paleoceanographic studies. The quantitative power of the δ 238 U proxy derives from the long marine residence time of uranium and the dominance of reduction in fractionating uranium isotopes during removal from seawater. The seawater δ 238 U value is therefore sensitive to the size of the anoxic sink, and by extension, the area of the seafloor overlain by anoxic waters. Leveraging the ability of carbonates to record and retain the seawater δ 238 U value, and the ubiquity of carbonate sediments in the geologic record, numerous studies have quantified seafloor anoxia across ocean anoxic events, mass extinctions, and global climatic changes. In most cases, forward models of marine uranium isotope mass balance have been used, illustrating potential histories of seafloor anoxia during these events. Here we show that there are multiple ways in which such forward modeling can lead to spurious inferences of anoxia, including (i) the poor sensitivity of the δ 238 U proxy when fractional anoxia is high, and (ii) the inherent bias in generating illustrative forward model outputs in stratigraphic sections with expected anoxic intervals. We thus explore inverse modeling approaches to constrain the most likely history of seafloor anoxia for a given δ 238 U dataset, and ultimately develop a framework for doing so using Bayesian inference via Markov Chain Monte Carlo simulation. We show that this approach can recover simulated trends, and further reconstruct marine anoxia for eight published δ 238 U datasets. We find that some previous interpretations of anoxic seafloor extent were inaccurate, either because steady state was improperly assumed, or because the illustrative forward models used were poor fits to the data. In order to overcome these issues in future work with the δ 238 U redox proxy, we have made this model publicly available, and also offer suggestions for the judicious use of forward models. By building on this framework, the future quantification of marine anoxia during transient environmental perturbations can be performed consistently, thereby facilitating robust comparison of anoxic extent between events.
Tools for the characterization of biomass at the nanometer scale

To take advantage of nanoscale features in plant cell walls and create our own nanos­ tructures based on plant biomass, we must make reliable measurements at the nanoscale. Although nanoscale measurement methods have expanded in recent years, not all these techniques are useful for soft, hydrophilic, nonconducting biomass specimens. Here we discuss those methods with the potential to be particularly useful in studying nanoscale properties of plant biomass. In contrast to most engineering materials, plant biomass structure changes with water availability. Water swells biomass, creating pores that transport enzymes and reagents into and out of the cell wall during processing. Therefore we begin with a description of basic interactions of water and biomass. Nanoscale accessibility and reactivity of the cell wall are often critical to bioprocessing, so we discuss several methods of evaluating these properties. This chapter also describes methods to measure cellulose crystallinity, because crystallinity affects properties and crystallites are an interesting material in them­ selves. Finally the chapter reviews microscopic and spectroscopic methods useful for the study of biomass at the nanoscale.
Knowledge discovery in oceanographic databases: issues of complications in data sources

Data mining or knowledge discovery refers to a variety of techniques having the intent of uncovering useful patterns and association from large databases. We have been working with data mining techniques for a variety of oceanographic data and have encountered a number of troublesome issues relative to available data. We describe the steps preparatory to data mining and three data mining techniques that we have applied to spatio-temporal data. We include a detailed review of various sources of geospatial, oceanographic and meteorological data and associated issues inherent in their use in knowledge discovery. We also provide issues relevant to the difficulties in providing an overall integration of this heterogeneous data for knowledge discovery.
Molecular Subtyping, Source Tracking, and Food Safety

This chapter focuses on the application of molecular subtyping methods for identifying and tracing sources of microbial pathogens in food and food-borne human diseases. It should be noted, however, that in addition to the food-borne pathogens, harmless or nonpathogenic microorganisms can also contaminate the food supply and contribute to spoilage. These microbes are generally part of the natural microbiota of raw foods and food products, which serves as an ideal growth medium for many organisms with nearly neutral pH, high water activity, and richness in nutrients. If left unchecked, growth of these harmless microorganisms on foods results in off odors and flavors and, ultimately, in an inedible food product. Many of the methods developed to inhibit the growth of nonpathogenic microbes in foods also restrict the growth of food-borne pathogens. The major advantage of pulsed-field gel electrophoresis (PFGE) profiling is that the technique can be widely applied to different bacterial species and is relatively simple and straightforward to perform in the laboratory. Outbreak investigation and epidemiological tracing have been the primary incentives encouraging the development of the PulseNet and FoodNet national systems for food-borne disease surveillance. In the future, the authors expect to see the application of new molecular genotyping systems with rapid throughput, such as those based on single-nucleotide polymorphisms, to generate high-quality genotypic data for microbial source tracking.
Fast multiplierless approximation of the DCT for MPEG-7 color layout descriptor

In this paper, the implementation of BinDCT, fast multiplier less approximation of the DCT, on MPEG-7 color layout descriptor is described and the performances of BinDCT, JPEG FDCT and MPEG-7 DCT are discussed is well. The new member of the MPEG family called MPEG-7, the multimedia content description interface, is imposed to deal with various audio visual informations available from many sources around the world. The purpose of MPEG-7 is to extract the multimedia description that can be used in various applications. One of the MPEG-descriptors, color layout descriptor, is explained in this paper.
The Study Designed by a Committee: Design of the Multisite Violence Prevention Project

This article describes the research design of the Multisite Violence Prevention Project (MVPP), organized and funded by the National Center for Injury Prevention and Control (NCIPC) at the Centers for Disease Control and Prevention (CDC). CDC's objectives, refined in the course of collaboration among investigators, were to evaluate the efficacy of universal and targeted interventions designed to produce change at the school level. The project's design was developed collaboratively, and is a 2 × 2 cluster-randomized true experimental design in which schools within four separate sites were assigned randomly to four conditions: (1) no-intervention control group, (2) universal intervention, (3) targeted intervention, and (4) combined universal and targeted interventions. A total of 37 schools are participating in this study with 8–12 schools per site. The impact of the interventions on two successive cohorts of sixth-grade students will be assessed based on multiple waves of data from multiple sources of information, including teachers, students, parents, and archival data. The nesting of students within teachers, families, schools and sites created a number of challenges for designing and implementing the study. The final design represents both resolution and compromise on a number of creative tensions existing in large-scale prevention trials, including tensions between cost and statistical power, and between internal and external validity. Strengths and limitations of the final design are discussed.
Construction and characterization of expression systems for the env gene of ts1, a mutant of Moloney murine leukemia virus-TB

A temperature-sensitive mutant of the Moloney murine leukemia virus-TB, ts1, causes hindlimb paralysis and immunodeficiency in mice. At the restrictive temperature, the envelope precursor polyprotein, gPr80env, is inefficiently processed intracellularly, and this is associated with the neurovirulence of ts1. To test the hypothesis that expression of the envelope proteins of ts1 alone without infectious virus production can induce paralysis, it is necessary to use either transmissible retroviral expression vectors or microinjection of eukaryotic gene expression plasmid to introduce the env gene of ts1 into germlines of mice. In this study, we have constructed three retrovirus vectors and three gene expression plasmids, all of which contain the env gene of ts1. By comparing the different expression systems, we found that one construct, pts1-env(F) can express the envelope proteins at a level comparable to the level expressed in ts1-infected cells. Furthermore, the expressed envelope proteins of pts1-env(F)-transfected cells possess the phenotypes of the proteins expressed by the env gene of ts1.
Influence of pregnancy upon hypertension induced in rats by sodium chloride and desoxycorticosterone.

Conclusions1. Desoxycorticosterone acetate (DCA) and sodium choloride, in amounts sufficient to cause hypetension do not interfere with conception, implantation or normal delivery in rats. 2. When pregnancy in superimposed upon DCA-sodium hypertension, the blood pressure and fluid balance are not affected. There may be a transient increase of proteinuria during the last third of pregnancy. 3. The failure of the elevated blood pressure to fall during late pregnancy, as it regularly does in experimenta renal hypertension, suggests a differece in the chemical mediation of the 2 types of hypertension.
Endpoint Selection and Relative (Versus Absolute) Risk Reporting in Published Medication Trials

BACKGROUND The use of surrogate and composite endpoints, disease-specific mortality as an endpoint, and relative (rather than absolute) risk reporting in clinical trials may produce results that are misleading or difficult to interpret.
Plasma tryptophan during weight restoration in patients with anorexia nervosa

Background Anorexia nervosa (AN) is a mental disorder characterized by low weight and concerns about body shape and weight. Disturbance in serotonin function has been described as central to the psychobiology of this disorder. Plasma tryptophan (TRP), the essential amino acid needed for serotonin production, is known to be low following acute caloric restriction but has not been measured during the course of refeeding. Methods Plasma TRP and other large neutral amino acids (LNAA) levels were measured in 26 female patients with AN and 15 control subjects. Patient levels were measured at admission for inpatient treatment, after 1 week of treatment, and upon weight restoration to weight ≥90% ideal body weight (IBW). For 17 patients, an additional assessment was made when weight reached 80% IBW. Plasma levels were obtained on one occasion from healthy control subjects. Results Plasma TRP and TRP/LNAA ratio increased significantly during refeeding process. Plasma TRP in patients was 46.88 nmol/mL (SD = 19.59) on admission and 55.54 nmol/L/mL (SD = 8.1) at normal weight, p Conclusions Plasma TRP normalizes during the course of refeeding, supporting the hypothesis that serotonin function is disturbed in patients with anorexia nervosa.
Quantitative effects of vegetation cover on wind erosion and soil nutrient loss in a desert grassland of southern New Mexico, USA

Wind is a key abiotic factor that influences the dynamics of arid and semiarid systems. We investigated two basic relationships on vegetation manipulation (grass cover reduction) plots at the Jornada Experimental Range in southern New Mexico: (1) wind erosion rates (horizontal mass flux and dust emission) versus vegetative cover, and (2) nutrient loss versus vegetative cover. The results indicate that wind erosion rates and nutrient loss by dust emission are strongly affected by plant cover; however, the importance of shrubs and grasses in reducing dust flux may not be equal. The dramatic increase of wind erosion between 75% grass cover reduction and 100% grass cover reduction suggests that sparsely distributed mesquites are relatively ineffective at reducing wind erosion and nutrient loss compared to grasses. Comparisons of nutrients between surface soils and wind blown dust indicate that aeolian transport is a major cause for the loss of soil nutrients in susceptible environments. We found that increased aeolian flux over three windy seasons (March 2004–July 2006) removed up to 25% of total organic carbon (TOC) and total nitrogen (TN) from the top 5 cm of soil, and about 60% of TOC and TN loss occurred in the first windy season (March–July 2004). The balance between net loss of nutrients by aeolian processes and the addition of nutrients by biotic processes changed from negative (net loss) to positive (net accumulation) between 50% grass cover reduction and 25% grass cover reduction. The estimated lifetime of surface soil TOC and TN of about 10 years on the plot with 100% grass cover reduction indicates that impacts of wind erosion on soil resources can occur on very short timescales.
Effect of Starch Encapsulation and Temperature on Volatilization of Atrazine and Alachlor

Volatilization of agricultural chemicals is one process whereby chemicals may enter into parts of the environment where they were not intended. Starch encapsulation of pesticides has been proposed as a way of modifying pesticide behavior in the soil environment. This study was conducted to assess how starch encapsulation and temperature affect volatilization of atrazine [6-chloro-N-thyl-N'-(1-methylethyl)-1,3,5-thazine-2,4-diamine] and alachlor [2-chloro-N-(2,6-diethylphenyl)-N-(methoxymethyl)acetamide]. Volatilization was measured using agroecosystem chambers as model systems
Conceptualizing the interdisciplinary diffusion and evolution of emerging fields: The case of systems biology

Abstract This paper contributes to the longitudinal study and representation of the diffusion of scholarly knowledge through bibliometrics. The case of systems biology is used to illustrate a means for considering the structure and different roles of journals in the diffusion of a relatively new field to diverse subject areas. Using a bipartite network analysis of journals and subject categories, a core–intermediary–periphery diffusion structure is detected through comparative analysis of betweenness centrality over time. Systems biology diffuses from a core of foundational, theoretical areas to more specific, applied, practical fields, most of which relate to human health. Next, cluster analysis is applied to subject category co-occurrence networks to longitudinally trace the movement of fields within the core–intermediary–periphery structure. The results of these analyses reveal patterns of systems biology's diffusion across both theoretical and applied fields, and are also used to suggest how the dynamics of a field's interdisciplinary evolution can be realized. The author concludes by presenting a typology for considering how journals may function to support attributes of the core–intermediary–periphery structure and diffusion patterns more broadly.
Enzyme conjugation to the polysaccharide chitosan: smart biocatalysts and biocatalytic hydrogels.

Laccase from Coriolopsis gallica was conjugated to the renewable biopolymer chitosan using carbodiimide chemistry. The laccase−chitosan conjugate was observed to offer three unique properties. Firs...
Structure-activity relationships of substituted N-benzyl piperidines in the GBR series: Synthesis of 4-(2-(bis(4-fluorophenyl)methoxy)ethyl)-1-(2-trifluoromethylbenzyl)piperidine, an allosteric modulator of the serotonin transporter.

Abstract A series of 4-(2-(bis(4-fluorophenyl)methoxy)ethyl)-(substituted benzyl) piperidines with substituents at the ortho and meta positions in the aromatic ring of the N -benzyl side chain were synthesized and their affinities and selectivities for the dopamine transporter (DAT), serotonin transporter (SERT), and norepinephrine transporter (NET) were determined. One analogue, 4-(2-(bis(4-fluorophenyl)methoxy)ethyl)-1-(2-trifluoromethylbenzyl)piperidine (the C 2 -trifluoromethyl substituted compound), has been found to act as an allosteric modulator of hSERT binding and function. It had little affinity for any of the transporters. Several compounds showed affinity for the DAT in the low nanomolar range and displayed a broad range of SERT/DAT selectivity ratios and very little affinity for the NET. The pharmacological tools provided by the availability of compounds with varying transporter affinity and selectivity could be used to obtain additional information about the properties a compound should have to act as a useful pharmacotherapeutic agent for cocaine addiction and help unravel the pharmacological mechanisms relevant to stimulant abuse.
How are we doing? Group-based economic assessments and African American political behavior

Using data from the National Black Election Study, this study tests the importance of group-based economic evaluations in driving African American political behavior. Group-based evaluations powerfully influence presidential approval and vote choice, even controlling for national and personal evaluations and a conception of “linked fate.” More importantly, group-based assessments exert a significant and independent influence on turnout, the central variable in black electoral politics. The results extend and reconsider the implications of group solidarity as a motivator of black political behavior and suggest that a revision of traditional notions of economic voting is in order, at least for African Americans.
Efficacy of combined surgery and irradiation for localized Ewings sarcoma family of tumors

Background Local tumor control for patients with Ewings sarcoma family of tumors (ESFT) is favorable when the primary tumor is resectable or small. Local failure rates for patients who received combined surgery and RT were reviewed to determine outcome and prognostic factors. Procedures We performed a retrospective review of all patients with localized ESFT treated with combined definitive surgery and RT between 1978 and 2001, at St. Jude Children's Research Hospital. Rates of local failure, survival, and prognostic factors for recurrence were determined in 39 patients who received combined local therapy. Systemic treatment included vincristine, actinomycin D, cyclophosphamide, and doxorubicin (6 patients), with the addition of ifosfamide and etoposide (33 patients). Results With a median follow-up of 8.7 years the 5- and 8-year survival estimates were 89.2 ± 5.4% and 82.8 ± 7.3%. The 8-year incidence of local failure was 10.8 ± 5.2%. The 8-year local failure rate for patients with positive surgical margins was 17% and for negative surgical margins 5% (P = 0.25). Overall survival was improved for patients with negative surgical margins (94 vs. 71%, P = 0.052). Tumor size, site, histologic response, and radiation dose did not significantly alter the rate of local failure. Conclusions Patients with ESFT managed with definitive surgery and irradiation have favorable local control rates. Even among patients with unfavorable prognostic factors local tumor control remained excellent. © 2004 Wiley-Liss, Inc.
An Island-Based Approach for Differential Expression Analysis

High-throughput mRNA sequencing (also known as RNA-Seq) promises to be the technique of choice for studying transcriptome profiles. This technique provides the ability to develop precise methodologies for transcript and gene expression quantification, novel transcript and exon discovery, and splice variant detection. One of the limitations of current RNA-Seq methods is the dependency on annotated biological features (e.g. exons, transcripts, genes) to detect expression differences across samples. This forces the identification of expression levels and the detection of significant changes to known genomic regions. Any significant changes that occur in unannotated regions will not be captured. To overcome this limitation, we developed a novel segmentation approach, Island-Based (IB), for analyzing differential expression in RNA-Seq and targeted sequencing (exome capture) data without specific knowledge of an isoform. The IB segmentation determines individual islands of expression based on windowed read counts that can be compared across experimental conditions to determine differential island expression. In order to detect differentially expressed genes, the significance of islands (p-values) are combined using Fisher's method. We tested and evaluated the performance of our approach by comparing it to the existing differentially expressed gene (DEG) methods: CuffDiff, DESeq, and edgeR using two benchmark MAQC RNA-Seq datasets. The IB algorithm outperforms all three methods in both datasets as illustrated by an increased auROC.
Circuits over monoids: a fault model, and a trade-off between testability and circuit delay

Abstract We introduce a new fault model for evaluation circuits and prefix circuits over a transformation monoid. For evaluation circuits we give a trade-off between the delay of the circuit and the number of test-inputs needed to detect faultiness.
Must the old and young compete for health care resources

The number of older persons in our society is increasing as the number of younger persons decreases. Expenditures on the young are decreasing and those on the elderly are increasing. Questions relating to the decisions that may be made in the process of allocation of resources for these competing gr
Interventions for patients, providers, and health care organizations

Clinicians and the organizations within which they practice play a major role in enabling patient participation in cancer screening and ensuring quality services. Guided by an ecologic framework, the authors summarize previous literature reviews and exemplary studies of breast, cervical, and colorectal cancer screening intervention studies conducted in health care settings. Lessons learned regarding interventions to maximize the potential of cancer screening are distilled. Four broad lessons learned emphasize that multiple levels of factors-public policy, organizational systems and practice settings, clinicians, and patients-influence cancer screening; that a diverse set of intervention strategies targeted at each of these levels can improve cancer screening rates; that the synergistic effects of multiple strategies often are most effective; and that targeting all components of the screening continuum is important. Recommendations are made for future research and practice, including priorities for intervention research specific to health care settings, the need to take research phases into consideration, the need for studies of health services delivery trends, and methods and measurement issues.
Anomalies in the structural and magneto-transport properties of thin films of Bi substituted LaCaMnO

The effects of Bi-substitution on structural, magnetic, and transport properties of polycrystalline and RF sputtered thin films of LaCaMnO are reported. Films of La0.62Bi0.05Ca0.33MnO3 sputtered on (1 1 1)Si are polycrystalline whereas textured films with (1 1 0) orientation are obtained for (1 0 0)Si. In bulk polycrystalline samples, Bi substitution leads to (i) a very small decrease in the lattice constant and (ii) a large reduction in the Curie temperature Tc (230 K vs. 240 K for La0.67Ca0.33MnO3). The films, however, show a 0.4% decrease in the lattice constant and a relatively high Tc (= 262–266 K) due to reduced MnOMn bond lengths. Although the magnetic parameters are identical for polycrystalline and oriented films, electrical resistivity ρ and MR data for the (1 1 0) textured films show the following anomalous features: (i) a semiconductor like conduction and the absence of the metal-semiconductor transition observed near Tc in polycrystalline bulk samples and thin films, (ii) a two-order of magnitude increase in low temperature ρ relative to the polycrystalline films and (iii) MR-values much higher than for polycrystalline films. These data are indicative of a giant anisotropy in the magneto-transport properties of thin films of the oxides.
Comparison of Continuum and Explicit Models of Solvation: Potentials of Mean Force for Alanine Dipeptide

We compute the potential of mean force (PMF) around the φ and ψ torsions of alanine dipeptide with a Poisson−Boltzmann (PB) method and compare these results to simulations in explicit water. The PB method, which includes an apolar solvation term, qualitatively reproduces the PMF profiles generated in the explicit solvent simulation at a markedly lower computational cost. These results motivate more extensive testing of continuum methods for the study of conformational and binding equilibria in solution.
Protein distribution in commercial wet- and dry-milled corn germ.

To identify high-valued coproducts from commercially processed corn germ, it was necessary to determine the effect of processing conditions on corn germ proteins. We found that significantly less protein was extracted from commercial wet-milled as compared to dry-milled corn germ using Tris, sodium dodecyl sulfate (SDS) buffer containing 14 mM 2-mercaptoethanol at 100 °C for 10 min. SDS−polyacrylamide gel electrophoresis (PAGE) revealed a number of proteins with molecular masses ranging from approximately 10 to 66 kDa for the dry-milled corn germ as compared to only a few significant protein bands centered around 23 kDa in the wet-milled corn germ. The protein content of the wet- and dry-milled corn germ was approximately the same; however, nonprotein nitrogen values were significantly greater for the wet-milled than for the dry-milled germ. The distribution of fractionated germ protein freshly excised from the embryo of yellow dent corn kernels was more similar to that of dry-milled than wet-milled corn....
Late DES thrombosis: A lot of smoke, very little fire?

Recent studies and editorials have stirred controversy and generated tremendous publicity in the lay press related to the safety of drug-eluting stents (DES) for the treatment of coronary artery disease. Questions have been raised regarding the risks of late, or very late stent thrombosis with DES. The purpose of this editorial and review of stent thrombosis is to illuminate some counterpoints to some of the attention surrounding the issues of late DES thrombosis. The risks of DES stent thrombosis versus BMS may have been overstated by flawed studies. Late stent thrombosis does occur with both BMS and DES, and may or may not be modestly higher with DES. The time course of very late “DES thrombosis,” suggests that peristent plaque ruptures and disease progression in the target vessel may cause some, or many of these events. There is still much to be learned about the biology of DES. Although there is a small risk of late thrombosis with DES, there is little question that this technology provides benefit to the vast majority of patients compared with prior revascularization strategies, using balloon angioplasty, BMS, or bypass surgery. Substantial resources should be devoted to creating more biocompatible DES systems, and to minimizing the risks of both early and late stent thrombosis. © 2007 Wiley-Liss, Inc.
Mass density of glassy Pd 80 Si 20 during low-temperature light ion irradiation

Changes in mass density of amorphous Pd{sub 80}Si{sub 20} were monitored in situ during irradiation with He{sup 2+} and H{sup +} ions at temperatures below 100 K and during subsequent thermal treatment. The mass density decreased with increasing ion fluence and exponentially approached a saturation value of -1.2%, corresponding to a recombination volume of 190 atomic volumes. The initial swelling rate was 2.3 atomic volumes/displaced atom. The mass density of the irradiated material increased during subsequent thermal treatment, and the irradiation-induced decrease of the mass density recovered completely at room temperature.
CARTOS II semi-automated nerve tracing : three-dimensional reconstruction from serial section micrographs

The paper describes the history of tracing activities in the Levinthal lab from 1965 to the present. It also focuses on the evolution of electron micrograph (EM) tracing from early hand tracing reconstruction to the current, nearly fully automated CARTOS II tracing system. The present hardware systems and tracing algorithms are described in detail. Also presented are the partial tracing results of one EM data set in two and three dimensions.
Fluid flow-induced prostaglandin E2 response of osteoblastic ROS 17/2.8 cells is gap junction-mediated and independent of cytosolic calcium

Abstract It has been well demonstrated that bone adapts to mechanical loading. To accomplish this at the cellular level, bone cells must be responsive to mechanical loading (mechanoresponsive). This can occur via such mechanisms as direct cell deformation or signal transduction via complex pathways involving chemotransport, hormone response, and/or gene expression, to name a few. Mechanotransduction is the process by which a bone cell senses a biophysical signal and elicits a response. While it has been demonstrated that bone cells can respond to a wide variety of biophysical signals including fluid flow, stretch, and magnetic fields, the exact pathways and mechanisms involved are not clearly understood. We postulated that gap junctions may play an important role in bone cell responsiveness. Gap junctions (GJ) are membrane-spanning channels that physically link cells and support the transport of small molecules and ions in the process of gap junctional intercellular communication (GJIC). In this study we examined the role of GJ and GJIC in mechanically stimulated osteoblastic cells. Following fluid flow stimulation, we quantified prostaglandin E 2 (PGE 2 ) (oscillatory flow) and cytosolic calcium (Ca 2+ ) (oscillatory and steady flow) responses in ROS 17/2.8 cells and a derivative of these cells expressing antisense cDNA for the gap junction protein connexin 43 (RCx16) possessing significantly different levels of GJIC. We found that the ROS17/2.8 cells possessing increased GJIC also exhibited increased PGE 2 release to the supernatant following oscillatory fluid flow stimulation in comparison to coupling-decreased RCx16 cells. Interestingly, we found that neither osteoblastic cell line responded to oscillatory or steady fluid flow stimulation with an increase in Ca 2+ . Thus, our results suggest that GJ and GJIC may be important in the mechanotransduction mechanisms by which PGE 2 is mechanically induced in osteoblastic cells independent of Ca 2+ .
Intraoperative determinants of infrainguinal bypass graft patency: A prospective study*

Objectives: To evaluate a number of currently available methods for intraoperative assessment of infrainguinal bypass grafts (IBG) in terms of detecting technical errors and predicting graft failure. Design: Prospective open clinical study. Methods: Forty-nine patients undergoing 54 consecutive IBG were studied. Intraoperatively, the following measurements were performed: distal pulse palpation (DPP), continuous wave Doppler (CWD), pulse volume recording (PVR), and ultrasonic volume flowmetry (UVF), followed by intraoperative angiography of the entire graft and runoff vessels. The outflow resistance was graded according to the guidelines of the Society for Vascular Surgery and International Society for Cardiovascular Surgery (SVS/ISCVS runoff score). Graft patency was determined noninvasively (PVR, colour Duplex) up to 12 months following surgery. Predictive values and likelihood ratios for the intraoperative tests in detecting a technical problem during the bypass procedure and in predicting early graft failure were calculated. Results: There were five immediate revisions for problems detected intraoperatively. Angiography did not identify any additional problems but assisted in the correct location of the problems detected by the other tests. DPP and CWD were highly significant indicators of the need for revision with likelihood ratios for a positive test of 14.7 ( p p p n = 39) failed in the first postoperative month. Conclusions: Simple CWD insonation of graft and anastomoses is the best intraoperative indicator for technical inadequacies after IBG. Routine intraoperative angiography is not necessary and intraoperative anatomical imaging may be reserved for situations in which noninvasive documentation of technical success is absent. Contrary to the intraoperative haemodynamic test results, the SVS/ISCVS runoff score is a good predictor of early graft failure.
R-CHOP strikes again with survival benefit in follicular lymphoma

Comment on Hiddemann et al, page [3725][1] Hiddemann and colleagues demonstrate improved response duration and overall survival with the addition of rituximab to CHOP, compared with CHOP alone, in symptomatic patients with untreated advanced-stage follicular lymphoma. The arrival of rituximab (R
Random occurrence of stimulated Raman scattering emission from liquid water microdroplets

Stimulated Raman scattering (SRS) spectra from micrometer-sized water droplets have been obtained in the range 2100 104 laser shots. Possible causes of these noteworthy emission features are discussed, including the difficulty of coupling weak spontaneous Raman emission to both the intense pump beam and the morphology-dependent resonances within the droplet.
Randomized double-blind comparison of nifedipine and isosorbide dinitrate in patients with coronary arterial spasm

The effects of nifedinpine and isosorbide dinitrate on the frequency of angina and consumption of nitroglycerin were studied in 19 patients with coronary arterial spasm. After a lead-in phase, the patients were randomized to treatment with either nifedipine or isosorbide dinitrate. After dose titration (40 to 120 mg/day) and evaluation, they were given the alternate therapy. During the initial segment of the double-blind phase, one patient died suddenly (nifedipine phase), one dropped out of the study (nifedipine phase) and another was unable to tolerate therapy (isosorbide dinitrate phase). In the other 16 patients, the mean frequency of angina was less during therapy with both nifedipine (0.69 episode/day, p less than 0.05) and isosorbide dinitrate (0.77 episode/day, p less than 0.05) phases than during the lead-in phase (1.71 episodes/day). The mean frequency of angina was similar in the nifedipine and isosorbide dinitrate phases. A 50 percent or greater decrease in frequency of angina compared with lead-in phase values occurred in 13 of 18 patients during treatment with nifedipine and in 10 of 16 during treatment with isosorbide dinitrate. Of the 16 patients who completed both double-blind phases, 7 showed greater improvement (that is, a 50 percent or greater decrease in frequency of angina) with nifedipine than with isosorbide dinitrate); 6 others showed greater improvement with isosorbide dinitrate, and the other 3 had a less than 50 percent difference in frequency of angina with the two drugs. These findings in a limited number of patients suggest that both nifedipine and isosorbide dinitrate are effective in certain patients with coronary spasm but that neither drug is clearly superior.
Modeling, Simulation, and Translation Framework for the Preclinical Development of Monoclonal Antibodies

The industry-wide biopharmaceutical (i.e., biologic, biotherapeutic) pipeline has been growing at an astonishing rate over the last decade with the proportion of approved new biological entities to new chemical entities on the rise. As biopharmaceuticals appear to be growing in complexity in terms of their structure and mechanism of action, so are interpretation, analysis, and prediction of their quantitative pharmacology. We present here a modeling and simulation (M&S) framework for the successful preclinical development of monoclonal antibodies (as an illustrative example of biopharmaceuticals) and discuss M&S strategies for its implementation. Critical activities during early discovery, lead optimization, and the selection of starting doses for the first-in-human study are discussed in the context of pharmacokinetic–pharmacodynamic (PKPD) and M&S. It was shown that these stages of preclinical development are and should be reliant on M&S activities including systems biology (SB), systems pharmacology (SP), and translational pharmacology (TP). SB, SP, and TP provide an integrated and rationalized framework for decision making during the preclinical development phase. In addition, they provide increased target and systems understanding, describe and interpret data generated in vitro and in vivo, predict human PKPD, and provide a rationalized approach to designing the first-in-human study.
Solvent motion and excited state decay in solutions of Cr(III) complexes

Abstract Thermal quenching of 2E in Cr(bpy)33+ (bpy = 2,2′-bipyridine) solutions where back-intersystem crossing is not important is compared with the quenching of Cr(NCS)63− and trans-Cr(NH3)2(NCS)4− in several solvents. Solvent motion enhances excited state relaxation whether or not back-intersystem crossing is a significant relaxation pathway. The relationship between motionally induced decay and the exponential or nonexponential character of the decay is discussed.