cssi/SciSciGPT-SciSciNet huggingface dataset:
Spatial Variation of Crustal Coda Q in California

Coda wave data from California microearthquakes were studied in order to delineate regional fluctuations of apparent crustal attenuation in the band 1.5 to 24 Hz. Apparent attenuation was estimated using a single back scattering model of coda waves. The coda wave data were restricted to ≤ 30 s following the origin time; this insures that crustal effects dominate the results as the backscattered shear waves thought to form the coda would not have had time to penetrate much deeper. Results indicate a strong variation in apparent crustal attenuation at high frequencies between the Franciscan and Salinian regions of central California and the Long Valley area of the Sierra Nevada. Although the coda Q measurements coincide at 1.5 Hz (Q c = 100), at 24 Hz there is a factor of four difference between the measurements made in Franciscan (Q c = 525) and Long Valley (Q c = 2100) with the Salinian midway between (Q c = 900). These are extremely large variations compared to measures of seismic velocities of comparable resolution, demonstrating the exceptional sensitivity of the high frequency coda Q measurement to regional geology. In addition, the frequency trend of the results is opposite to that seen in a compilation of coda Q measurements made worldwide by other authors which tend to converge at high and diverge at low frequencies, however, the worldwide results generally were obtained without limiting the coda lengths and probably reflect upper mantle rather than crustal properties. Our results match those expected due to scattering in random media represented by Von Karman autocorrelation functions of orders 1/2 to 1/3. The Von Karman medium of order 1/3 corresponding to the Franciscan coda Q measurement contains greater amounts of high wavenumber fluctuations. This indicates relatively large medium fluctuations with wavelengths on the order of 100 m in the highly deformed crust associated with the Franciscan, however, the influence of scattering on the coda Q measurement is currently a matter of controversy.
Nominations open for presidential science awards

Nominations are now being accepted for two presidential science award programs. For the Presidential Awards for Excellence in Science, Mathematics, and Engineering Mentoring, nominations are being accepted until 5 June 2013. The award, which was established by the White House in 1995, recognizes U.S. citizens or permanent residents and U.S. organizations that have demonstrated excellence in mentoring individuals from groups that are underrepresented in science, technology, engineering, and mathematics (STEM) education and the workforce.
Induction of α-Glucosidase in Mycoplasma laidlawii A

MYCOPLASMA are a group of microorganisms distinct from bacteria, blue green algae and viruses. In size, their genomes are intermediate between those of viruses and bacteria and similar to those of the trachoma agents1. We report here the discovery of an α-glucosidase inducible by maltose in Mycoplasma laidlawii A. This is the first demonstration of enzyme synthesis control in the order Mycoplasmatales.
Magmatic heat and the El Niño cycle

Large submarine lava flows with apparent volumes exceeding 10 km3 have recently been imaged on the deep ocean floor in various parts of the Pacific by means of GLORIA and SeaMarc side-looking sonar surveys. Such flows may produce thermal anomalies large enough to perturb the cyclic processes of the ocean and could be a factor in the genesis of El Nino phenomena. We find that known volume rates of mid-ocean magma production could generate repetitive thermal anomalies as large as 10% of the average El Nino sea surface anomaly at intervals of about 5 years (the mean interval of El Nino events between 1935 and 1984). Likewise, estimated rates of eruption, cooling of lava on the seafloor, and transfer of heat to the near-surface environment could reasonably produce a thermal anomaly comparable to that associated with El Nino. Larger magmatic events, associated with fluctuations in the total magmatic power and seismicity along the East Pacific Rise, are possible at longer intervals and may explain the extreme size of some El Nino events, such as that of 1982–1983.
Dendritic cells and aging: consequences for autoimmunity

The immune system has evolved to mount immune responses against foreign pathogens and to remain silent against self-antigens. A balance between immunity and tolerance is required as any disturbance may result in chronic inflammation or autoimmunity. Dendritic cells (DCs) actively participate in maintaining this balance. Under steady-state conditions, DCs remain in an immature state and do not mount an immune response against circulating self-antigens in the periphery, which maintains a state of tolerance. By contrast, foreign antigens result in DC maturation and DC-induced T-cell activation. Inappropriate maturation of DCs due to infections or tissue injury may cause alterations in the balance between the tolerogenic and immunogenic functions of DCs and instigate the development of autoimmune diseases. This article provides an overview of the effects of advancing age on DC functions and their implications in autoimmunity.
Adolf Seilacher's fossil record

Adolf (Dolf) Seilacher, who died earlier this year at the age of 89, was a major figure in palaeontology on both sides of the Atlantic. His interests were diverse, including trace fossils, the processes involved in exceptional preservation, and the evolution of invertebrate morphology. But it is for his views on the nature of the extraordinary fossils of the Ediacaran that he is perhaps best known. His ideas—compelling and provocative—will continue to stimulate research for years to come, not least through the wide use of his terminology (e.g. Lagerstatten, morphodynamics, constructional morphology, vendobiont).
SNF5/INI1 deficiency redefines chromatin remodeling complex composition during tumor development

Malignant rhabdoid tumors (MRT), a pediatric cancer that most frequently appears in the kidney and brain, generally lack SNF5 (SMARCB1/INI1), a subunit of the SWI/SNF chromatin-remodeling complex. Recent studies have established that multiple SWI/SNF complexes exist due to the presence or absence of different complex members. Therefore, the effect of SNF5 loss upon SWI/SNF complex formation was investigated in human MRT cells. MRT cells and primary human tumors exhibited reduced levels of many complex proteins. Furthermore, reexpression of SNF5 increased SWI/SNF complex protein levels without concomitant increases in mRNA. Proteomic analysis, using mass spectrometry, of MRT cells before and after SNF5 reexpression indicated the recruitment of different components into the complex along with the expulsion of others. IP–Western blotting confirmed these results and demonstrated similar changes in other MRT cell lines. Finally, reduced expression of SNF5 in normal human fibroblasts led to altered levels of these same complex members. These data establish that SNF5 loss during MRT development alters the repertoire of available SWI/SNF complexes, generally disrupting those associated with cellular differentiation. These findings support a model where SNF5 inactivation blocks the conversion of growth-promoting SWI/SNF complexes to differentiation-inducing ones. Therefore, restoration of these complexes in tumors cells provides an attractive approach for the treatment of MRTs. Implications: SNF5 loss dramatically alters SWI/SNF complex composition and prevents formation of complexes required for cellular differentiation. Mol Cancer Res; 12(11); 1574–85. ©2014 AACR . This article is featured in Highlights of This Issue, [p. 1533][1] [1]: /lookup/volpage/12/1533?iss=11
The hidden costs of outsourcing

Many outsourcing arrangements fail to deliver the expected cost savings. Why is this so? The author argues that management hasn't calculated the total cost of outsourcing, which includes your risks—and he shows you how to do it. © 2008 Wiley Periodicals, Inc.
Zone of Transition: A Potential Source of Error in Tumor Volume Estimation

The average width of the transition zone is in the range of the width of a single pixel on a typical full field of view CT scan; how this is accounted for, considering that it surrounds the entire tumor, can substantially change a volume estimate, especially for smaller tumors.
Allelic variation at alcohol metabolism genes (ADH1B, ADH1C, ALDH2) and alcohol dependence in an American Indian population

Enzymes encoded by two gene families, alco- hol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH), mediate alcohol metabolism in humans. Allelic variants have been identified that alter metabolic rates and influence risk for alcoholism. Specifically, ADH1B*47His (previously ADH2-2) and ALDH2-2 have been shown to confer protection against alcoholism, presumably through accumulation of acetaldehyde in the blood and a resultant 'flushing response' to alcohol consumption. In the current study, variants at ADH1B(previously ADH2), ADH1C (pre- viously ADH3), and ALDH2 were assayed in DNA ex- tracts from participants belonging to a Southwest Ameri- can Indian tribe (n=490) with a high prevalence of alco- holism. Each subject underwent a clinical interview for diagnosis of alcohol dependence, as well as evaluation of intermediate phenotypes such as binge drinking and flush- ing response to alcohol consumption. Detailed haplotypes were constructed and tested against alcohol dependence and related intermediate phenotypes using both associa- tion and linkage analysis. ADH and ALDH variants were also assayed in three Asian and one African population (no clinical data) in order to provide an evolutionary context for the haplotype data. Both linkage and association analysis identified several ADH1C alleles and a neighboring mi- crosatellite marker that affected risk of alcohol depen- dence and were also related to binge drinking. These data strengthen the support for ADH as a candidate locus for alcohol dependence and suggest further productive study.
BORRELIA SP. INFECTION IN COYOTES, BLACK-TAILED JACK RABBITS AND DESERT COTTONTAILS IN SOUTHERN TEXAS

Coyotes (Canis latrans) from southern Texas were sampled for antibodies to Borrelia burgdorferi from 1980 to 1986; black-tailed jack rabbits (Lepus californicus) and desert cottontails (Sylvilagus audubonii) were sampled in 1986. Coyote fetuses, adult coyote kidneys, and black-tailed jack rabbit and desert cottontail kidneys were cultured for B. burgdorferi in 1986. Results of indirect immunofluorescent antibody (IFA) tests for B. burgdorferi in coyotes were as follows (number positive at a dilution of ≥l:128/number tested): 1980 (0 of 30), 1981 (0 of 21), 1982 (0 of 53), 1983 (0 of 78), 1984 (47 of 97), 1985 (20 of 88), and 1986 (42 of 80). Eight of 26 black-tailed jack rabbits and two of seven desert cottontails tested in 1986 had IFA titers to B. burgdorferi of ≥1:128. Borrelia burgdorferi was isolated from one of five coyote fetuses, three of 31 adult coyote kidneys, and two of 10 black-tailed jack rabbit kidneys in 1986. These results indicate that B. burgdorferi infection has been present in coyotes...
Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast

A general method for the dynamic control of single gene expression in eukaryotes, with no off-target effects, is a long-sought tool for molecular and systems biologists. We engineered two artificial transcription factors (ATFs) that contain Cys(2)His(2) zinc-finger DNA-binding domains of either the mouse transcription factor Zif268 (9 bp of specificity) or a rationally designed array of four zinc fingers (12 bp of specificity). These domains were expressed as fusions to the human estrogen receptor and VP16 activation domain. The ATFs can rapidly induce a single gene driven by a synthetic promoter in response to introduction of an otherwise inert hormone with no detectable off-target effects. In the absence of inducer, the synthetic promoter is inactive and the regulated gene product is not detected. Following addition of inducer, transcripts are induced >50-fold within 15 min. We present a quantitative characterization of these ATFs and provide constructs for making their implementation straightforward. These new tools allow for the elucidation of regulatory network elements dynamically, which we demonstrate with a major metabolic regulator, Gcn4p.
p‐bromobenzazide as a reagent for the identification of alcohols

p-Bromobenzazide, from nitrous acid and p-bromobenzhydrazide, was condensed in hot ligroin solution with various kinds of alcohols, giving solid, crystalline urethanes with distinct melting points. These urethanes are considered as suitable derivatives for the identification of alcohols.
Effect of nuclear radiation on the electrical properties of chemical double layer capacitors

The effects of nuclear radiation on the electrical properties of chemical double-layer capacitors are determined. The capacitors were irradiated in a 2-MW nuclear reactor to different fluence levels. The exposure rate was 2.2*10/sup 10/ n/cm/sup 2/-s for thermal neutrons, 9.52*10/sup 8/ n/cm/sup 2/-s for fast neutrons (>3 MeV), and 1.47*10/sup 6/ rad/h for gamma radiation. The properties measured during and after irradiation included the capacitance, equivalent series resistance, and open-circuit voltage. The postirradiation effect on the leakage current was also determined. It was found that, while the capacitance increased during irradiation, the equivalent series resistance and the open-circuit voltage decreased slightly during irradiation. Changes in these properties, however, were not permanent, as was evident from postirradiation measurements. The leakage current did not show any significant change with radiation. The results indicate that chemical double-layer capacitors can be suitably used as a backup power source in electronic equipment operating in a radiation environment with total fluences up to 4.05*10/sup 14/ n/cm/sup 2/. >
Modifying Genetic Disease

We are all genetic time bombs on the brink of disaster. The 1000 Genomes Project ([www.1000genomes.org][1]) revealed that the average healthy person harbors ~400 damaging mutations and ~2 bona fide disease-causing mutations in their genome; yet, we remain, for the most part, healthy. For this reason, instead of on disease genes more focus should be placed on modifier genes and protective alleles that prevent the genetic bomb from going off. Drugs that target those modifier gene pathways can then be developed. In this vein, Park et al. searched for modifiers of ataxin 1 (ATXN1) to treat spinocerebellar ataxia type 1 (SCA1)—a rare and fatal disease. SCA1 is a neurodegenerative disease affecting the cerebellum and spinal cord that is caused by polyglutamine expansions in the gene encoding ATXN1. Reducing levels of ATXN1 protein can reverse the disease in animal models. Park et al. therefore screened for genetic modifiers of ATXN1 levels in human cell lines and in flies ( Drosophila ). By intersecting the results from the two screens, they were able to identify 10 highly conserved modifier genes that reduced ATXN1 levels and suppressed an eye-degeneration phenotype in flies expressing a mutant form of ATXN-1. The most enriched pathway among the modifier genes was the RAS/mitogen-activated protein kinase (MAPK) pathway. As such, the authors devised genetic strategies to inhibit components of the RAS/MAPK signaling pathway in a Drosophila SCA1 model carrying a mutant version of atxn1 . Reduction of these modifier genes lowered the levels of ATXN1, prevented eye degeneration, and improved motor behavior in the flies. In human cells, pharmacological inhibition of MAPK signaling components reduced ATXN1 levels. They further found that MSK1 (mitogen- and stress-activated protein kinase) regulates ATXN1 levels by phosphorylating and stabilizing the protein. Genetically reducing MSK1 levels in a mouse model of SCA1 partially rescued neurodegenerative processes and improved motor performance. This effort demonstrates the importance of studying modifier genes to develop new treatment strategies for seemingly intractable genetic diseases. The study also highlights the power of intersecting approaches from different model organisms in this effort. The next step will be to evaluate the efficacy of the available drugs that inhibit the RAS/MAPK pathway in mouse models and in patients, in order to translate these findings for SCA1 treatment. J. Park et al. , RAS-MAPK-MSK1 pathway modulates ataxin 1 protein levels and toxicity in SCA1. Nature 498 , 325–331 (2013). [[Pub Med]][2] [1]: http://www.1000genomes.org/ [2]: http://www.ncbi.nlm.nih.gov/pubmed/23719381
Paving the Way for Future Race Research Exploring the Racial Mechanisms Within a Color-Blind, Racialized Social System

In a day when many are fatigued with discourse on racism, discrimination, and inequality but others face a socially and politically trenchant White backlash against the gains of the civil rights mo...
EET counselor takes on student role

An undergraduate advisor in the Electrical Engineering Technology Department at Purdue University challenged herself to participate as a student in the introductory electrical circuits course. The initial purpose for a counselor with a nontechnical background to undertake such a task was to become a better counselor for the technical majors. The objectives were to gain a better understanding of the fundamentals of the academic program and to gain a better appreciation of the freshman year experience in a lab-oriented major. The counselor essentially become a part-time student and completed all aspects of the course that are required of the enrolled students: attending both lectures and labs and completing all student assignments. With the involvement and support of the course instructor, and the interaction of the students, a deeper than anticipated insight into the student experience was gained. The counselor and teacher had new insights into the academic program, classroom experience, and counseling strategies. The shared experiences and insights gained are described. >
Are midwater shrimp trapped in the craters of submarine volcanoes by hydrothermal venting

The biology of Kick'em Jenny (KEJ) submarine volcano, part of the Lesser Antilles volcanic arc and located off the coast of Grenada in the Caribbean Sea, was studied during a cruise in 2003. Hydrothermal venting and an associated biological assemblage were discovered in the volcanic crater (~250 m depth). Warm water with bubbling gas emanated through rock fissures and sediments. Shrimp (some of them swimming) were clustered at vents, while other individuals lay immobile on sediments. The shrimp fauna consisted of 3 mesopelagic species that had no prior record of benthic or vent association. We suggest that these midwater shrimp, from deeper water populations offshore, were trapped within the crater during their downward diel vertical migration. It is unknown whether they then succumbed to the hostile vent environment (immobile individuals) or whether they are potentially opportunistic vent residents (active individuals). Given the abundance of submarine arc volcanoes worldwide, this phenomenon suggests that volcanic arcs could be important interaction sites between oceanic midwater and vent communities. © 2005 Elsevier Ltd. All rights reserved.
Sequential Multiresolution Trajectory Optimization Schemes for Problems with Moving Targets

In this paper, we present two sequential multiresolution trajectory optimization algorithms for solving problems with moving targets and dynamically changing environments. For such problems, high accuracy is desirable only in the immediate future, yet the ultimate mission objectives should be accommodated as well. An intelligent trajectory generation algorithm is proposed, enabled by the introduction of the idea of multigrid temporal resolution to solve the associated trajectory optimization problem on a nonuniform grid across time. The grid is adapted to the immediate future and to potential discontinuities in the state and control variables.
Minimally invasive high-speed imaging of sarcomere contractile dynamics in mice and humans

Sarcomeres are the basic contractile units of striated muscle. Our knowledge about sarcomere dynamics has primarily come from in vitro studies of muscle fibres and analysis of optical diffraction patterns obtained from living muscles. Both approaches involve highly invasive procedures and neither allows examination of individual sarcomeres in live subjects. Here we report direct visualization of individual sarcomeres and their dynamical length variations using minimally invasive optical microendoscopy to observe second-harmonic frequencies of light generated in the muscle fibres of live mice and humans. Using microendoscopes as small as 350 microm in diameter, we imaged individual sarcomeres in both passive and activated muscle. Our measurements permit in vivo characterization of sarcomere length changes that occur with alterations in body posture and visualization of local variations in sarcomere length not apparent in aggregate length determinations. High-speed data acquisition enabled observation of sarcomere contractile dynamics with millisecond-scale resolution. These experiments point the way to in vivo imaging studies demonstrating how sarcomere performance varies with physical conditioning and physiological state, as well as imaging diagnostics revealing how neuromuscular diseases affect contractile dynamics.
Deploying design for Six Sigma™ in new product development

An overview Six Sigmatrade and Design for Six Sigmatrade (DFSS) were presented, with the differences between the two illustrated. DFSS tools, methodology and their applications within the Motorola Penangpsilas pilot programs were presented. Critical Parameter Management (CPM) was introduced to ensure the new radio design has sufficient margin in meeting the critical voice of customer (VOC). The derivation of transfer functions using design of experiment (DOE) and response surface methodology (RSM) in optimising design parameters were discussed. Lessons learned from using the DFSS tools and methodology as applied in the pilot projects were discussed and the benefits resulted from its applications in meeting the design margins and customer requirements were presented. Lastly, the benefits and opportunities of DFSS implementation were presented, before concluded with the successful implementation of DFSS.
Observation of Microwaves Mixing in Air Glow Plasma

An experiment on the generation of X-band heterodynes due to mixing of C-band microwave and S-band microwave in an air glow plasma is reported. The measured mixing coefficient agrees with the predictions based on the kinetic theory.
A Real-Time Analysis of Traumatic Brain Injury from T2 Weighted Magnetic Resonance Images Using a Symmetry-Based Algorithm

In this chapter, we provide an automated computational algorithm for detection of traumatic brain injury (TBI) from T2-weighted magnetic resonance (MRI) images. The algorithm uses a combination of brain symmetry and 3D connectivity in order to detect the regions of injury. The images are preprocessed by removing all non-brain tissue components. The ability of our symmetry-based algorithm to detect the TBI lesion is compared to manual detection. While manual detection is very operator-dependent which can introduce intra- and inter-operator error, the automated detection method does not have these limitations and can perform skull stripping and lesion detection in real-time and more rapidly than manual detection. The symmetry-based algorithm was able to detect the lesion in all TBI animal groups with no false positives when it was tested versus a naive animal control group.
ChR2 transgenic animals in peripheral sensory system: Sensing light as various sensations

Since the introduction of Channelrhodopsin-2 (ChR2) to neuroscience, optogenetics technology was developed, making it possible to activate specific neurons or circuits with spatial and temporal precision. Various ChR2 transgenic animal models have been generated and are playing important roles in revealing the mechanisms of neural activities, mapping neural circuits, controlling the behaviors of animals as well as exploring new strategy for treating the neurological diseases in both central and peripheral nervous system. An animal including humans senses environments through Aristotle's five senses (sight, hearing, smell, taste and touch). Usually, each sense is associated with a kind of sensory organ (eyes, ears, nose, tongue and skin). Is it possible that one could hear light, smell light, taste light and touch light? When ChR2 is targeted to different peripheral sensory neurons by viral vectors or generating ChR2 transgenic animals, the animals can sense the light as various sensations such as hearing, touch, pain, smell and taste. In this review, we focus on ChR2 transgenic animals in the peripheral nervous system. Firstly the working principle of ChR2 as an optogenetic actuator is simply described. Then the current transgenic animal lines where ChR2 was expressed in peripheral sensory neurons are presented and the findings obtained by these animal models are reviewed.
Nuclear transport in vitro.

Summary In this paper, progress towards the goal of understanding communication between the nucleus and cytoplasm using an in vitro system is reviewed. To probe the mechanism of nuclear targeting, we developed an in vitro transport system and have begun to dissect the highly selective process of nuclear transport. The basic parameters of transport were defined using an easily isolated nuclear protein, nucleoplasmin. To study the interaction of nuclear targeting signals with the pore, an artificial nuclear transport substrate was constructed, which consists of human serum albumin coupled to the signal sequence of the SV40 T-antigen. A similar peptide–protein conjugate was made using a mutant signal sequence. These conjugates were fluorescently labeled and/or tagged with gold and tested for transport in the in vitro system. High levels of nuclear transport of the wild-type signal sequence-containing protein were observed, while no transport of the mutant signal sequence-containing protein was seen. Thus, the in vitro system correctly recognizes the single amino acid change between the wild-type and mutant signal sequences. We found that the observed nuclear transport was completely dependent on the presence of ATP. Using the in vitro system we identified a specific inhibitor of nuclear transport, the lectin wheat germ agglutinin (WGA), which we find binds directly to the nuclear pore. Probing blots of nuclear proteins with 125I-WGA identified a family of nuclear pore glycoproteins, including one major glycoprotein of 62K (K = 103Mr) molecular weight. With the inhibitor and the in vitro assay, it has been possible to experimentally separate nuclear transport into two steps: (1) a step in which the signal sequence-bearing protein binds to the pore, followed by (2) a step in which the protein translocates through the pore. It is this second step which is the ATP-dependent step of transport, since pore binding but not translocation was seen to occur in the absence of ATP.
Foodies & food tourism

Foodies & food tourism is a 239 page volume that includes 9 chapters. The topics cover a range of food tourism concepts including the perspectives of the foodie and food tourism; the who and what o...
Rethinking sensitivity analysis of nuclear simulations with topology

In nuclear engineering, understanding the safety margins of the nuclear reactor via simulations is arguably of paramount importance in predicting and preventing nuclear accidents. It is therefore crucial to perform sensitivity analysis to understand how changes in the model inputs affect the outputs. Modern nuclear simulation tools rely on numerical representations of the sensitivity information — inherently lacking in visual encodings — offering limited effectiveness in communicating and exploring the generated data. In this paper, we design a framework for sensitivity analysis and visualization of multidimensional nuclear simulation data using partition-based, topology-inspired regression models and report on its efficacy. We rely on the established Morse-Smale regression technique, which allows us to partition the domain into monotonic regions where easily interpretable linear models can be used to assess the influence of inputs on the output variability. The underlying computation is augmented with an intuitive and interactive visual design to effectively communicate sensitivity information to nuclear scientists. Our framework is being deployed into the multipurpose probabilistic risk assessment and uncertainty quantification framework RAVEN (Reactor Analysis and Virtual Control Environment). We evaluate our framework using a simulation dataset studying nuclear fuel performance.
Lewis acid-base interactions between platinum(ii) diaryl complexes and bis(perfluorophenyl)zinc: strongly accelerated reductive elimination induced by a Z-type ligand.

Z-type interactions between bis(perfluorophenyl)zinc and platinum(II) diaryl complexes supported by 1,10-phenanthroline (phen), 2,2′-bipyridine (bpy), and bis(dimethylphosphino)ethane (dmpe) ligands are reported. In the solid state, the nature of the Pt–Zn interaction depends on the bidentate ligand; the phen-supported complex exhibits an unsupported Pt–Zn bond, while the dmpe derivative features additional bridging aryl interactions. A strongly accelerated rate of reductive elimination is observed for phen- and bpy-supported complexes, while aryl exchange between Pt and Zn is observed for the dmpe complex.
Abstract P2-01-01: Next generation sequencing of circulating tumor DNA to predict recurrence in triple-negative breast cancer patients with residual disease after neoadjuvant chemotherapy

Background: Incorporation of next-generation sequencing to detect plasma-derived tumor DNA (ptDNA) is emerging as a popular method for tumor genotyping and for monitoring therapeutic response. The vast majority of studies so far have focused on detecting ptDNA from patients with metastatic disease. Herein, we tested whether ptDNA could be used as a biomarker to predict relapse in triple-negative breast cancer (TNBC) patients with residual disease after neoadjuvant chemotherapy and surgery. Methods: BRE09-146 was a Phase II clinical trial that randomized TNBC patients with residual disease after neoadjuvant chemotherapy to Cisplatin or Cisplatin+Rucaparib. From the combination arm, 1ml of plasma was collected at four predefined time points post-surgery. In total, 39 patients with matched tumor, blood, and plasma were analyzed. Extracted DNA underwent library preparation and amplification using the Ion Ampliseq Oncomine Research Panel which consists of 134 cancer genes that are well-known to be mutated in cancer. Samples were then sequenced on an Ion Proton next-generation sequencer to at least 2500X coverage followed by bioinformatic analyses using the Torrent Variant Caller. Results: We first detected high-quality somatic mutations in primary tumors. TP53 mutations were the most prevalent (70%) followed by AKT1 (8%). Somatic mutation frequencies in our trial were congruent with publically-available mutation data of TNBCs from The Cancer Genome Atlas. Using these somatic mutations, we then analyzed the plasma-sequencing data to detect the same mutations in the circulation. Out of 39 patients, 14 patients had a clinical relapse (median follow-up for disease free survival = 24 months). Of the 14 patients, we were able to detect somatic ptDNA in 4 patients (3 TP53 mutations, 1 AKT mutation). Notably, all 4 patients had a rapid recurrence (0.3, 4.0, 5.3, and 8.9 months). ptDNA-sequencing was unable to detect distant recurrence. The combination of a paucity of ptDNA molecules in the circulation of patients who have no evidence of disease along with a limited amount of plasma available per patient are potential factors for the inability to detect distant recurrence. Conclusions: Next-generation ptDNA-sequencing of triple-negative breast cancer patients after neoadjuvant chemotherapy and surgery can detect rapid-recurrence but sensitivity to detect distant recurrence is limited. Studies to increase sensitivity by incorporating mutation calling from ptRNA along with ptDNA are currently underway. Citation Format: Chen Y-H, Hancock BA, Solzak JP, Miller KD, Radovich M. Next generation sequencing of circulating tumor DNA to predict recurrence in triple-negative breast cancer patients with residual disease after neoadjuvant chemotherapy. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-01-01.
The newborn chest.

Newer therapeutic techniques in the respiratory management of preterm and full-term neonates have resulted in improved survival, particularly in those infants who have respiratory distress syndrome, severe pneumonia, and surgical lesions of the chest. Although respiratory distress syndrome is being seen less frequently because of improved ventilatory management and the use of surfactant replacement therapy, the increased survival of preterm infants has resulted in an increased incidence of bronchopulmonary dysplasia, still a frequently seen pulmonary abnormality. Children who have severe pulmonary disease related to diaphragmatic hernia, meconium aspiration pneumonia, and infectious pneumonia are treated with extracorporeal membrane oxygenation, resulting in a higher survival rate and better outcome. Other abnormalities of the lung, including pneumonia, are seen in both preterm and full-term infants, have characteristic radiographic appearances, and require prompt antibiotic treatment.
Open repair of cardiac defects in neonates and young infants

This article provides a general description of many aspects of the perioperative and operative management of neonates and young infants with congenital heart disease. Operative technique and results are described in more detail for the most important defects.
Inadequate Hydration, BMI, and Obesity Among US Adults: NHANES 2009-2012

PURPOSE Improving hydration is a strategy commonly used by clinicians to prevent overeating with the goal of promoting a healthy weight among patients. The relationship between weight status and hydration, however, is unclear. Our objective was to assess the relationship between inadequate hydration and BMI and inadequate hydration and obesity among adults in the United States. METHODS Our study used a nationally representative sample from the National Health and Nutrition Examination Survey (NHANES) 2009 to 2012, and included adults aged 18 to 64 years. The primary outcome of interest was body mass index (BMI), measured in continuous values and also categorized as obese (BMI ≥30) or not (BMI RESULTS In this nationally representative sample (n = 9,528; weighted n = 193.7 million), 50.8% were women, 64.5% were non-Hispanic white, and the mean age was 41 years. Mean urine osmolality was 631.4 mOsm/kg (SD = 236.2 mOsm/kg); 32.6% of the sample was inadequately hydrated. In adjusted models, adults who were inadequately hydrated had higher BMIs (1.32 kg/m2; 95% CI, 0.85–1.79; P CONCLUSION We found a significant association between inadequate hydration and elevated BMI and inadequate hydration and obesity, even after controlling for confounders. This relationship has not previously been shown on a population level and suggests that water, an essential nutrient, may deserve greater focus in weight management research and clinical strategies.
New Frontiers in Machine Learning for Predictive User Modeling

Publisher Summary Ambient intelligence often requires sensing and prediction of internal user state. However, reliably recognizing internal user state during interaction with a computer or a smart interface is a challenge, often complicated by sensor noise and drop-out and by the difficulty of obtaining labels for the true states involved. This chapter describes a range of recent advances in machine learning that can help alleviate these problems. Techniques such as semi-supervised and active learning specifically address the issue of building predictive user models when the training data is scarce and relatively hard to collect. This chapter discusses these techniques in the context of many different applications that require systems that predict users' affective and cognitive states. The illustrated schemes can be used in any scenario that needs analysis and machine learning from data obtained from multiple channels and having very few labels and annotations. Many research application scenarios encounter difficulties due to multimodal data or having to annotate an enormous corpus with labels of interest. There are many applications in different domains, such as sensor networks, social networks, and other multimodal scenarios, where the proposed method can be used effectively. Because many models that handle such data are probabilistic, an interesting question is how to extend the discriminative framework to handle them. The techniques mentioned in this chapter can be mixed and matched to produce novel schemes for handling multimodal channels in conjunction with tackling the problem of labeled data scarcity.
SBS suppression and coherence properties of a flat top optical spectrum in a high power fiber amplifier

In this paper we report the generation of flat top optical spectrum using an arbitrary waveform generator to increase the SBS threshold in high power optical fiber amplifiers. The optical spectrum consists of a number of discrete spectral lines, ranging from 16 to 380, within the bandwidth of 2GHz, corresponding to line spacing between 133 MHz and 5 MHz. These discrete spectral lines correspond to a PRBS pattern of n = 4 to n = 8. The SBS threshold and coherence properties of the flat top spectrum are measured and compared to that of the filtered PRBS in a kilowatt class fiber amplifier. It is experimentally demonstrated that for large frequency line spacing, the flat top spectrum significantly outperforms the corresponding filtered PRBS, but as the line spacing is decreased to less than the Brillouin bandwidth, the two modulation waveforms have similar enhancement factors in the SBS threshold due to the enhanced crosstalk between neighboring frequency components.
Spinal racemose cysticercosis: case report and review

ABSTRACTCysticercosis is a common helminthic infection worldwide, endemic in Central and South America, sub-Saharan Africa, and Southeast Asia. Neurocysticercosis typically involves brain parenchyma, subarachnoid space, and the ventricular system. Although the spinal cord is frequently involved in patients with parenchymal neurocysticercosis, isolated spinal involvement is rare, occurring in only 1–3% of patients.We report a case of racemose spinal neurocysticercosis with brain parenchyma involvement in a 49-year-old Mexican man, who presented with unsteady gait and bilateral arm numbness and weakness. Magnetic resonance imaging revealed multiseptated cystic lesions in the upper cervical spinal canal and nonenhancing intradural extramedullary cystic lesions in the thoracic spine. The patient underwent sub-occipital craniectomy with decompression, followed by a course of steroids and albendazole. Pathology confirmed the diagnosis of neurocysticercosis, and the patient’s symptoms resolved after treatment.We...
System-level considerations for modeling space-based quantum key distribution architectures

Quantum Key Distribution (QKD) is a revolutionary technology which leverages the laws of quantum mechanics to distribute cryptographic keying material between two parties with theoretically unconditional security. Terrestrial QKD systems are limited to distances of <200 km in both optical fiber and line-of-sight free-space configurations due to severe losses during single photon propagation and the curvature of the Earth. Thus, the feasibility of fielding a low Earth orbit (LEO) QKD satellite to overcome this limitation is being explored. Moreover, in August 2016, the Chinese Academy of Sciences successfully launched the world's first QKD satellite. However, many of the practical engineering performance and security tradeoffs associated with space-based QKD are not well understood for global secure key distribution. This paper presents several system-level considerations for modeling and studying space-based QKD architectures and systems. More specifically, this paper explores the behaviors and requirements that researchers must examine to develop a model for studying the effectiveness of QKD between LEO satellites and ground stations.
Digital Storytelling: Communicating Academic Research Beyond the Academy

BRIEF SESSION DESCRIPTION:Digital storytelling has the ability to take knowledge and ideas to reach a broader audience, and can be utilized in the classroom setting to provide students with opportunities to learn digital skills as well as content. This teaching demonstration will present strategies for integrating digital storytelling into the classroom, and include digital stories created by three graduate students. as examples.________________________________________________________________FULL ABSTRACT:AÂ Digital storytelling can be many things A¢â¬â narrative, interactive, linear, nonlinear, immersive, artistic, educational. We do not, however, typically think of it as a tool for communicating academic research. What happens when we use digital storytelling to present our academic knowledge and ideas and to reach broader audiences? When we use it in the classroom to teach digital skills as well as content?This teaching demo will explore these questions and more, including practical strategies for integrating digital storytelling into the classroom across disciplines and rubrics for assessing digital storytelling assignments.Three graduate students will show short clips of the digital stories they created based on their research and will talk about their learning process. Topics include slavery at Mt. Vernon and the nature of historical research, first generation students at George Mason University, and the holistic review process for college applications. These students will address the skills they learned, including the craft of storytelling, storytelling tools, understanding audience, and communicating academic research in an accessible, compelling way. They will talk about the value of creating something usable and sharable, the impact on their learning, and developing practical, transferable skills.AÂ We will model how digital storytelling can be used in small assignments focused on discrete topics and individual assignments as well as for larger projects.AÂ Faculty from a range of disciplines will learn how to use digital storytelling in their own courses with an emphasis on small, discrete assignments. Faculty will learn how to integrate small digital projects and to think about how these can help achieve specific learning goals.
Erosion and refilling of the plasmasphere during a geomagnetic storm modeled by a neural network

We present a history-dependent model of the equatorial plasma density of the inner magnetosphere using a feedforward neural network with two hidden layers. As the model inputs, we take locations and time series of SYM-H, AL, and F10.7 indices. By considering not only the instantaneous values but also the past values of geomagnetic and solar indices, the model is history dependent on levels of geomagnetic and solar activity. The modeled electron density is continuous both spatially and temporally so that the evolution of the density can be studied (such as plasmaspheric refilling). The model is trained using the electron density inferred from the spacecraft potential from three THEMIS probes. The equatorial electron density is shown to be accurately reconstructed with a correlation coefficient of r ~ 0.953 between data and model target. Since the model is history dependent, it succeeds in reconstructing various density features and dynamic behaviors, such as the quiet time plasmasphere, erosion and recovery of the plasmasphere, as well as the plume formation during a storm on 4 February 2011. Our model may provide unprecedented insight into the behavior of the equatorial density at any time and location; as an example we show the inferred refilling rate from our model and compare it to previous estimates.
Lillian McMurry and the Blues Contracts of Trumpet Records

Trumpet Records was a Jackson, Mississippi-based record label established and run by Lillian McMurry from 1950 until it folded in 1955. This article draws on archival material to evaluate the progression of the contracts entered into by Trumpet Records with its blues artists, arguing that this demonstrates the evolving contractual understanding of a young record label, showing increasing sophistication and an awareness of some of the potential pitfalls of signing artists. The contracts of Trumpet Records, when taken together with the correspondence of the label’s head with her artists, also show a commitment to fairness and a level of scrupulousness and honesty not often seen in the industry. The article also examines the legal dispute between Sherman Johnson and Trumpet Records, which reached the Mississippi Supreme Court. The article further turns to the subsequent copyright infringement of a number of Trumpet Record recordings by European record labels in the 1970s, which sheds light on the widespread practice of piracy prevalent in relation to older blues recordings.
A viscous quantum hydrodynamics model based on dynamic density functional theory

Dynamic density functional theory (DDFT) is emerging as a useful theoretical technique for modeling the dynamics of correlated systems. We extend DDFT to quantum systems for application to dense plasmas through a quantum hydrodynamics (QHD) approach. The DDFT-based QHD approach includes correlations in the the equation of state self-consistently, satisfies sum rules and includes irreversibility arising from collisions. While QHD can be used generally to model non-equilibrium, heterogeneous plasmas, we employ the DDFT-QHD framework to generate a model for the electronic dynamic structure factor, which offers an avenue for measuring hydrodynamic properties, such as transport coefficients via x-ray Thomson scattering.
Efficient and broadband single-mode waveguide coupling of electrically injected optical antenna based nanoled

We propose a novel structure to provide broadband and efficient single-mode waveguide coupling of the output of an electrically injected slot antenna based nanoLED. Using 3D FDTD simulations, we show it is possible to achieve 90% waveguide coupling with greater than a 380nm 1dB bandwidth.
Importance of Symmetry and Conformational Flexibility in DNA Structure for Understanding Protein-DNA Interactions

During the past few years, there has been a growing realization that two aspects of DNA structure, namely, its symmetry and its conformational flexibility, play important roles in protein-DNA interactions involved in genetic regulation. This chapter reviews evidence along these lines, beginning with our structural studies of drug intercalation (these studies have given direct structural information concerning the roles of symmetry and conformational flexibility in DNA structure in a variety of drug-DNA interactions), enlarging on this theme with a discussion of the nature of DNA breathing and DNA denaturation, and ending with discussions of specific protein-DNA interactions that involve various aspects of DNA symmetry and flexibility—that is, histone-DNA interactions in chromatin, RNA polymerase-promoter recognition, operator-repressor recognition, and so on. No attempt is made to review the wealth of nucleotide sequence information currently available; rather, specific examples of protein-DNA interactions are discussed in detail and these will serve to illustrate the general principles involved.