cssi/SciSciGPT-SciSciNet huggingface dataset:
Frozen robust multiarray analysis (fRMA)

Robust multiarray analysis (RMA) is the most widely used preprocessing algorithm for Affymetrix and Nimblegen gene expression microarrays. RMA performs background correction, normalization, and summarization in a modular way. The last 2 steps require multiple arrays to be analyzed simultaneously. The ability to borrow information across samples provides RMA various advantages. For example, the summarization step fits a parametric model that accounts for probe effects, assumed to be fixed across arrays, and improves outlier detection. Residuals, obtained from the fitted model, permit the creation of useful quality metrics. However, the dependence on multiple arrays has 2 drawbacks: (1) RMA cannot be used in clinical settings where samples must be processed individually or in small batches and (2) data sets preprocessed separately are not comparable. We propose a preprocessing algorithm, frozen RMA (fRMA), which allows one to analyze microarrays individually or in small batches and then combine the data for analysis. This is accomplished by utilizing information from the large publicly available microarray databases. In particular, estimates of probe-specific effects and variances are precomputed and frozen. Then, with new data sets, these are used in concert with information from the new arrays to normalize and summarize the data. We find that fRMA is comparable to RMA when the data are analyzed as a single batch and outperforms RMA when analyzing multiple batches. The methods described here are implemented in the R package fRMA and are currently available for download from the software section of http://rafalab.jhsph.edu.
The limits of global scanning worm detectors in the presence of background noise

Internet worms cause billions of dollars in damage each year. To combat them, researchers have been exploring global worm detection systems to spot a new random scanning worm outbreak quickly. These systems passively listen for worm probes on unused IP addresses, looking for anomalous increases in probe traffic to distinguish the emergence of a new worm from background Internet noise.In this paper, we use analytic modeling, simulation, and measurement to understand how background noise impacts the detection ability of global scanning worm detectors. We investigate the relationship between the average background noise level, the number of IP addresses monitored, and the detection latency for two classes of global scanning worm detectors: scan packet-based and victims-based schemes. Our results show how worm detection latency degrades as a function of the background noise level. To compensate, global scanning worm detectors can increase the number of IP addresses that they monitor. However, given the growth trend of background noise levels, the number of IP addresses which must be monitored may quickly become unreasonable. Because of this, we conclude that global scanning worm detection schemes are unlikely to be competitive with local scanning and signature-based worm detection schemes.
An Emergent Phenomenon of American Indian Postsecondary Transition and Retention.

This study examined 21 American Indian students’ postsecondary transition and retention experiences through a phenomenological methodology. Postsecondary transition is the process of leaving home and adjusting to postsecondary education. Postsecondary retention is achieving success and remaining at a university for at least 6 months. Data sources included individual interviews, journal analysis, and document analysis. The 10 emergent themes described an interconnected phenomenon centered on institutional, social, and interpersonal dimensions.
The Specificity of Innate Immune Responses Is Enforced by Repression of Interferon Response Elements by NF-κB p50

The specific binding of transcription factors to cognate sequence elements is thought to be critical for the generation of specific gene expression programs. Members of the nuclear factor κB (NF-κB) and interferon (IFN) regulatory factor (IRF) transcription factor families bind to the κB site and the IFN response element (IRE), respectively, of target genes, and they are activated in macrophages after exposure to pathogens. However, how these factors produce pathogen-specific inflammatory and immune responses remains poorly understood. Combining top-down and bottom-up systems biology approaches, we have identified the NF-κB p50 homodimer as a regulator of IRF responses. Unbiased genome-wide expression and biochemical and structural analyses revealed that the p50 homodimer repressed a subset of IFN-inducible genes through a previously uncharacterized subclass of guanine-rich IRE (G-IRE) sequences. Mathematical modeling predicted that the p50 homodimer might enforce the stimulus specificity of composite promoters. Indeed, the production of the antiviral regulator IFN-β was rendered stimulus-specific by the binding of the p50 homodimer to the G-IRE–containing IFN β enhancer to suppress cytotoxic IFN signaling. Specifically, a deficiency in p50 resulted in the inappropriate production of IFN-β in response to bacterial DNA sensed by Toll-like receptor 9. This role for the NF-κB p50 homodimer in enforcing the specificity of the cellular response to pathogens by binding to a subset of IRE sequences alters our understanding of how the NF-κB and IRF signaling systems cooperate to regulate antimicrobial immunity.
Establishment and characterization of a lens epithelial cell line from an eight year old rabbit

Although information is available on the in vit-ro properties of lens epithelia of young adult animals from several species, few, if any reports document the conditions required for the initiation and long-term culture of lens epithelium from animals beyond their medium life-span. We report here on the conditions required for the culture of lens cells from an 8 year old rabbit. New Zealand White rabbits have a median life-span of approximately 7 years. Primary culture was initiated in MEM supplemented with 10% rabbit serum. Cells reached confluency within 25 days, responded to serum in a dose dependent manner and had an average doubling time of 23 h during the logarithmic growth phase. Cells increased in number in a dose dependent manner when insulin, insulin growth factor, epidermal growth factor (EGF), or fibroblast growth factor (FGF) was added to the culture medium. Thus, lens epithelia from this very old rabbit retained the ability to respond to highly purified growth factors. Cells exposed to a medi...
Comparison of unit-specific and hospital-wide antibiograms: potential implications for selection of empirical antimicrobial therapy.

Objective. To identify differences between unit-specific and hospital-wide antibiograms and to determine the potential impact of these differences on selection of empirical antimicrobial therapy. Setting. A 625-bed tertiary care medical center. Methods. Antimicrobial susceptibility results were collected for all inpatient clinical bacterial isolates recovered over a 3-year period; isolates were categorized by the hospital location of the patient at the time of sampling and by the anatomic site from which the isolate was recovered. Antibiograms from each unit were compiled for the most commonly isolated organisms and were compared to the hospital-wide antibiogram. Results. A total of 9,970 bacterial isolates were evaluated in this study, including 2,646 enterococcal isolates, 2,806 S. aureus isolates, 2,795 E. coli isolates, and 1,723 Pseudomonas aeruginosa isolates. The percentages of bacterial isolates resistant to antimicrobials were significantly higher in the medical ICU and surgical ICU than the hospital-wide antibiogram would have predicted, whereas the percentages of isolates susceptible to antimicrobials were significantly higher in the non-ICU units, compared with the hospital overall. However, on general medicine units, the prevalence of susceptibility to levofloxacin was significantly lower than that for the hospital overall. Conclusions. Unit-specific antibiograms are important for making informed decisions about empirical antimicrobial therapy, because the hospital-wide antibiogram may mask important differences in susceptibility rates across different units. These differences may have important implications for selecting the optimal empirical antimicrobial therapy.
Linalool: a novel natural anti-inflammatory agent?: Commentary on "Anti-inflammatory effects of linalool in RAW 264.7 macrophages and lipopolysaccharide-induced lung injury model".

DOI of original article: 10.1016/j.jss.2012.1 * Corresponding author. Department of Surg Tel.: þ1 513 558 8467; fax: þ1 513 558 3474. E-mail address: prittsta@ucmail.uc.edu (T 0022-4804/$ e see front matter a 2013 Elsev http://dx.doi.org/10.1016/j.jss.2013.02.014 Proinflammatory states are widely implicated in both acute and chronic disease processes. Severe acute systemic inflammation is at least partially responsible for shock and acute lung injury, and therapeutic options to curb the proinflammatory responses are limited. Sustained release of proinflammatory mediators by macrophages and other leukocyte subtypes is the hallmark of autoimmune illnesses. In addition to nonspecific immunosuppressants, targeted therapies to reduce inflammation via inhibition of cytokine release are available for some of these illnesses, including Crohn disease and rheumatoid arthritis. However, the subsequent risk of infection with these medications is significant, which limits their clinical use. Linalool is a terpene alcohol that occurs naturally in several edible plant species. It is used in soaps, oils, and other topical products, but has not been evaluated previously as a therapeutic. Its role as an inflammatory mediator is unknown. Based on the antimicrobial and anxiolytic properties of
Responses to Drying of Recalcitrant Seeds of Quercus nigra L.

Abstract It has been suggested that rate of desiccation can influence the expression of recalcitrant behaviour in seeds, thus complicating the task of determining which seeds are truly recalcitrant. The objective of this study was to see if variable rates of desiccation influenced such behaviour inQuercus nigraL., a tree seed known to be recalcitrant. Acorn moisture content, leachate conductivity, and germination were determined at various times during desiccation at three rates at 27 and 40°C. Moisture contents and germination decreased as the severity of desiccation increased. Leachate conductivity increased slightly but was not a sensitive indicator of loss of viability. The critical (lethal) moisture content for these acorns was 10–15%, although rehydration within 48 h of reaching this level prevented death in about 25% of the acorns. At 27°C any desiccation treatment that produced losses of 30–50mg of moisture per g of acorn dry weight per day should be suitable as a test for recalcitrance in the genus. Apparent physiological or fungal damage at 40°C rules out the higher temperature for such a test.
Bacteria induce osteoclastogenesis via an osteoblast-independent pathway.

Bacteria or their products may cause chronic inflammation and subsequent bone loss. This inflammation and bone loss may be associated with significant morbidity in chronic otitis media, periodontitis, endodontic lesions, and loosening of orthopedic implants caused by lipopolysaccharide (LPS)-contaminated implant particles. Currently, it is not clear how bacteria or endotoxin-induced bone resorption occurs and what cell types are involved. Here we report that Porphyromonas gingivalis, a periodontal pathogen, and Escherichia coli LPS induce osteoclastic cell formation from murine leukocytes in the absence of osteoblasts. In contrast, stimulation with parathyroid hormone had no effect. These multinucleated, tartrate-resistant acid phosphatase-positive cells were positive for receptor activator of NF-κB (RANK), the receptor for osteoprotegerin ligand (OPGL), also known as RANK ligand (RANKL). Blocking antibodies demonstrated that their formation was dependent upon expression of OPGL and, to a lesser extent, on tumor necrosis factor alpha. Mononuclear cells represented a significant source of OPGL production. In vivo, P. gingivalis injection stimulated OPGL expression in both mononuclear leukocytes and osteoblastic cells. Thus, these findings describe a pathway by which bacteria could enhance osteolysis independently of osteoblasts and suggest that the mix of cells that participate in inflammatory and physiologic bone resorption may be different. This may give insight into new targets of therapeutic intervention.
Transcriptional profiling defines the roles of ERK and p38 kinases in epidermal keratinocytes.

Epidermal keratinocytes respond to extracellular influences by activating cytoplasmic signal transduction pathways that change gene expression. Using pathway-specific transcriptional profiling, we identified the genes regulated by two such pathways, p38 and ERK. These pathways are at the fulcrum of epidermal differentiation, proliferative and inflammatory skin diseases. We used SB203580 and PD98059 as specific inhibitors and Affymetrix Hu133Av2 microarrays, to identify the genes regulated after 1, 4, 24, and 48 h and compared them to genes regulated by JNK. Unexpectedly, inhibition of MAPK pathways is compensated by activation of the NFκB pathway and suppression of the DUSP enzymes. Both pathways promote epidermal differentiation; however, there is a surprising disconnect between the expression of steroid synthesis enzymes and differentiation markers. The p38 pathway induces the expression of extracellular matrix and proliferation-associated genes, while suppressing microtubule-associated genes. The ERK pathway induces nuclear envelope and mRNA splicing proteins, while suppressing steroid synthesis and mitochondrial energy production enzymes. Transcription factors SRY, c-FOS, and N-Myc are the principal targets of the p38 pathway, Elk-1 SAP1 and HLH2 of ERK, while FREAC-4, ARNT and USF are shared. The results suggest a list of targets potentially useful in therapeutic interventions in cutaneous diseases and wound healing. J. Cell. Physiol. 215: 292–308, 2008. © 2008 Wiley-Liss, Inc.
The Pediatric Eye Disease Investigator Group

Introduction and Background: The Pediatric Eye Disease Investigator Group is a network of pediatric eye care providers undertaking clinical trials with National Eye Institute support. The network includes university- and community-based providers. Methods: Randomized and observation studies have involved refining the best amblyopia treatment in children from 3 to less than 18 years of age, observation of the behavior of early-onset esotropia, treatment of primary congenital nasolacrimal duct obstruction, and observation of the stability of strabismic angle in esotropia. Conclusions: To date 16 studies have been undertaken enrolling 5064 children and teens.
EXPERIMENTS WITH COMPUTERIZED SELF-ADMINISTRATIVE ACTIVITY SURVEY

The process of activity scheduling is crucial to the understanding of travel behavior changes. In-depth research is urgently needed to unearth this process. A new computer program, REACT!, was developed to collect household activity scheduling data for this purpose. The program is implemented as a stand-alone program with Internet connectivity for remote data transmission. It also contains a geographic information system for location identification and a special feature that traces the decisions in the scheduling process. A pilot study was conducted in Irvine, California, to evaluate the program's performance. Preliminary analysis validated the program's capability of guiding participants to complete data entry tasks on their own; thus, the objective of reducing the cost of human resources for such a computerized survey is achieved. Other positive results were obtained regarding the objectives of reducing instrumental biases and expanding program capabilities. Areas for improvement were identified in the pilot study. On the basis of the findings, REACT! represents an ideal platform for a computerized household survey that can produce data for activity-based travel models.
The role of gape-limitation in intraguild predation between endangered Mohave tui chub and non-native western mosquitofish

Intraguild predation (IGP) is a mechanism that may facilitate the co-existence of native species with non-native invasive species. We conducted laboratory predation trials to assess the role of predator gape-limitation in the context of IGP between the endangered Mohave tui chub (Siphateles bicolor mohavensis) and invasive western mosquitofish (Gambusia affinis). Larval tui chubs had significantly lower (v 2 = 74.74; P < 0.001) survival in the presence of female mosquitofish (10.0%) than in the presence of male mosquitofish (73.3%). Reciprocally, adult tui chubs preyed upon adult mosquitofish, causing a significantly lower (v 2 = 11.33; P < 0.001) survival for male mosquitofish (60%) compared to female mosquitofish survival (96.7%). Vulnerability modelling revealed that mosquitofish with a body depth < 4.6 mm and a larval tui chub with a body depth < 1.2 mm were completely vulnerable to predation by adult Mohave tui chub and adult mosquitofish, respectively. IGP in this study system is size-structured based on gape-size limitation and may have some conservation implications for the recovery of endangered Mohave tui chub. Our findings also provide an important caveat to the dogmatic view of mosquitofish as a threat whenever they invade. It is important to note that many previous studies that reported negative impacts of mosquitofish involved native species with relatively small body sizes, often the same size as mosquitofish.
Some inequalities for the trieste theory of unstable-particle decay

The relation between two integral equations of the Trieste theory of unstable-particle decay is discussed and then rigorous inequalities are obtained for the dependence of the observed lifetime on the parameters of the measuring environment and for the deviation of the observed nondecay probability from exponential form.
The Eventuality of the Digital

The article seeks to serve as ‘event’ in the sense understood by Alain Badiou: working together, in a way that breaks with the current order of knowledge production, towards a shared vision of scholarly and public access to our cultural heritage. Discussing a digital project that does not yet exist, The COVE or The Central Online Victorian Educator, the article imagines the possibilities for such a project and calls on readers of 19 to join in the creation of this online, collective venture.
Experimental facility for development of high-temperature reactor technology: instrumentation needs and challenges

A high-temperature, multi-fluid, multi-loop test facility is under development at the Idaho National Laboratory for support of thermal hydraulic materials, and system integration research for high-temperature reactors. The experimental facility includes a high-temperature helium loop, a liquid salt loop, and a hot water/steam loop. The three loops will be thermally coupled through an intermediate heat exchanger (IHX) and a secondary heat exchanger (SHX). Research topics to be addressed include the characterization and performance evaluation of candidate compact heat exchangers such as printed circuit heat exchangers (PCHEs) at prototypical operating conditions. Each loop will also include an interchangeable high-temperature test section that can be customized to address specific research issues associated with each working fluid. This paper also discusses needs and challenges associated with advanced instrumentation for the multi-loop facility, which could be further applied to advanced high-temperature reactors. Based on its relevance to advanced reactor systems, the new facility has been named the Advanced Reactor Technology Integral System Test (ARTIST) facility. A preliminary design configuration of the ARTIST facility will be presented with the required design and operating characteristics of the various components. The initial configuration will include a high-temperature (750 °C), high-pressure (7 MPa) helium loop thermally integrated with a molten fluoride salt (KF-ZrF4 ) flow loop operating at low pressure (0.2 MPa), at a temperature of ∼450 °C. The salt loop will be thermally integrated with the steam/water loop operating at PWR conditions. Experiment design challenges include identifying suitable materials and components that will withstand the required loop operating conditions. The instrumentation needs to be highly accurate (negligible drift) in measuring operational data for extended periods of times, as data collected will be used for code and model verification and validation, one of the key purposes for the loop. The experimental facility will provide a much-needed database for successful development of advanced reactors and provide insight into the needs and challenges in instrumentation for advanced high-temperature reactors.
POSIX and Object Distributed Storage Systems Performance Comparison Studies With Real-Life Scenarios in an Experimental Data Taking Context Leveraging OpenStack Swift & Ceph

The STAR online computing infrastructure has become an intensive dynamic system used for first-hand data collection and analysis resulting in a dense collection of data output. As we have transitioned to our current state, inefficient, limited storage systems have become an impediment to fast feedback to online shift crews. Motivation for a centrally accessible, scalable and redundant distributed storage system had become a necessity in this environment. OpenStack Swift Object Storage and Ceph Object Storage are two eye-opening technologies as community use and development have led to success elsewhere. In this contribution, OpenStack Swift and Ceph have been put to the test with single and parallel I/O tests, emulating real world scenarios for data processing and workflows. The Ceph file system storage, offering a POSIX compliant file system mounted similarly to an NFS share was of particular interest as it aligned with our requirements and was retained as our solution. I/O performance tests were run against the Ceph POSIX file system and have presented surprising results indicating true potential for fast I/O and reliability. STAR'S online compute farm historical use has been for job submission and first hand data analysis. The goal of reusing the online compute farm to maintain a storage cluster and job submission will be an efficient use of the current infrastructure.
Applications of Transformation Theory: A Legacy from Zolotarev (1847–1878)

What we are concerned with is, roughly, the generalization to the elliptic case of the familiar multiple angle formulas of elementary trigonometry such as $$\begin{array}{l} \cos \,2\theta = 2{\cos ^2}\,\theta \, - \,1;\,\tan \,2\theta = \frac{{2\,\tan \theta }}{{1 - {{\tan }^2}\theta }};\\ \sin \,2\theta = 2\,\sin \,\theta \cos \, \in = 2\sin \,\theta \sqrt {\left( {1 - {{\sin }^2}\theta } \right)} \end{array}$$ (which are respectively polynomial, rational, algebraic). More generally we have $$\cos \,{\rm{n}}\theta = {2^{n - 1}}\left[ {{{\cos }^n}\theta - \frac{1}{4}\,{{\cos }^{n - 2}}\,\theta \, + \, \ldots } \right]$$ which we can also express as a Chebyshev polynomial: $${{\rm{T}}_{\rm{n}}}\left( {\rm{x}} \right) = {\rm{cos}}\left( {{\rm{n}}\,{\rm{arccos}}\,{\rm{x}}} \right) = {{\rm{2}}^{{\rm{n}} - {\rm{1}}}}\left[ {{{\rm{x}}^{\rm{n}}} - \frac{{\rm{1}}}{{\rm{4}}}{\rm{n}}{{\rm{x}}^{{\rm{n}} - {\rm{2}}}}\,{\rm{ + }}\,{\rm{ \ldots }}} \right] = {{\rm{2}}^{{\rm{n}} - {\rm{1}}}}{\rm{ }}{{\rm{\tilde T}}_{\rm{n}}}\left( {\rm{x}} \right)$$
Erythropoiesis in hypothyroidism.

SummaryThe purpose of this study was to clarify the role which disordered iron metabolism and alterations in the homeostatic regulation of red cell production play in hypothyroid anemia. Following ...
Dynamic Analysis of a Planar Mechanism With Variable Topology

There is a demand for mechanisms with variable topology (MVTs) that can perform multiple tasks with the least amount of actuators. These devices have the ability to provide numerous motion profiles within one device. In this paper, a specific planar MVT was dynamically analyzed. This mechanism functions as a RRRP mechanism (i.e., slider-crank) in one configuration and as a RRRR mechanism (i.e., crank-crank) in the other. The kinematics and kinetics of the RRRP and RRRR configurations were analyzed with a Lagrangian approach. The resulting equations were coded both in equation form and in Matlab SimMechanics then compared. A method for transitioning between configurations was also developed. These equations could be used to develop an applicable controller and principles for synthesizing future MVTs.Copyright © 2015 by ASME
Interactive Visualization: Insight Through Inquiry, by Bill Ferster. Cambridge, MA: MIT Press, 2012. 275 pp. $42.00 hardcover. ISBN 978262018159 hardcover

It has been nearly 50 years since we entered the Information Age, a time “in which information has become a commodity that is quickly and widely disseminated and easily available especially through...
Effects of Ligand Geometry on the Photophysical Properties of Photoluminescent Eu(III) and Sm(III) 1-Hydroxypyridin-2-one Complexes in Aqueous Solution

A series of 10 tetradentate 1-hydroxy-pyridin-2-one (1,2-HOPO) ligands and corresponding eight-coordinated photoluminescent Eu(III) and Sm(III) complexes were prepared. Generally, the ligands differ by the linear (nLI) aliphatic linker length, from 2 to 8 methylene units between the bidentate 1,2-HOPO chelator units. The photoluminescent quantum yields (Φtot) were found to vary with the linker length, and the same trend was observed for the Eu(III) and Sm(III) complexes. The 2LI and 5LI bridged complexes are the brightest (Φtotxe). The change in ligand wrapping pattern between 2LI and 5LI complexes observed by X-ray diffraction (XRD) is further supported by density functional theory (DFT) calculations. The bimodal Φtot trends of the Eu(III) and Sm(III) complexes are rationalized by the change in ligand wrapping pattern as the bridge (nLI) is increased in length.
Condensed Tannins in Plant Defense: A Perspective on Classical Theories

Classical theories of condensed tannin-herbivore interactions should be reassesed. Condensed tannins may act in ways apart from digestion inhibition and may even act as metabolic toxins outside of the digestive system. Recent research has also questioned the generalized nature of condensed tannins as plant defenses; some condensed tannins are more deleterious to herbivores than others. In cases where condensed tannins do act as defensive compounds, however, animals may learn through experience rather than instinctively avoid high tannin content plants.
OPTIMAL SEQUENTIAL DECISIONS IN PROBLEMS INVOLVING MORE THAN ONE DECISION MAKER

Publisher Summary This chapter discusses optimal sequential decisions in problems involving more than one decision maker. It presents an initial exploration into the question of what information is necessary for Bayesians to specify to play a sequential game against each other. The chapter describes a game in which there are two players who take turns making decisions. It also discusses extensions to problems involving more than two players, games in which the moves are made simultaneously by the two players rather than alternatingly, or in which the order of play is not certain.
A Prospective Randomized Comparison of Contralateral Snare Versus Retrograde Gate Cannulation in Endovascular Aneurysm Repair

Abstract Objective The objective of this study was to compare snare vs the standard retrograde gate cannulation method during endovascular aneurysm repair to determine the most efficient technique and to evaluate whether time was affected by graft design or the surgeon's experience. Methods This was a prospective randomized study involving single-center elective endovascular aneurysm repairs. Patients were randomized to the snare or retrograde group in a 1:1 ratio. The initial method was attempted for 15 minutes; if it was unsuccessful, the team switched to the alternative technique for an additional 15 minutes. The protocol continued until success was achieved. Data collected on demographic, anatomic, and procedural factors were analyzed for statistically significant differences. Results A total of 101 patients were included. Average age was 75.3 years, and 82% were male; 49 patients were randomized to snare and 52 to retrograde cannulation. The groups were overall similar. Median cannulation times were 3.9 minutes for the snare and 2.7 minutes for the retrograde technique ( P = .13). The snare group attempts were successful within the initial 15-minute period in all but one patient (98% success). In the retrograde group, 5 of the 52 (10%) crossed over to snare. This difference did not reach statistical significance ( P = .11). A difference was seen in the extremes of cannulation times. The surgeon's experience and graft design were not found to have significant effects on cannulation times. Further analysis of the retrograde group patients with long cannulation time found a relative breakpoint at the 5-minute mark. In those exceeding this time mark, the chance of eventual cannulation within 15 minutes dropped to 67%. In this group, median time to cannulation was 12.2 minutes for retrograde compared with 7.1 minutes for snare after crossover. Conclusions Gate cannulation was successful using both methods with no statistical difference between the two in median time. Retrograde cannulation was found to be more likely to have short times. If cannulation by retrograde technique had not been achieved in the first 5 minutes, the chances of eventual success dropped significantly, and crossover to snare was more efficient. This finding suggests that one should consider an alternative method of gate cannulation if it has not been accomplished within this time.
The Characterization of Atomically Precise Nanoclusters Using X-Ray Absorption Spectroscopy

The XAS toolbox (EXAFS, XANES, theoretical calculations, in situ measurements) is used in a variety of applications to determine the structure and electronic properties of atomically precise nanoclusters (APNCs). The analysis using the EXAFS part of the XAS spectrum involves models that are based on atomic packing (e.g., fcc, icosahedra) or surface effects. Theoretical methods based on DFT can improve the understanding of disorder effects on the EXAFS measurements. In comparative experiments, the effect of solvation and of the ligands (density of ligands, different ligands) is discussed. It was found that the strength of the Au–thiol bonding can lead to relaxation effects that reduce the contraction of Au–Au bonds in the core. Changes in structure could be observed for solvation and catalytic reaction with the application of in situ measurements in specifically designed reactors. Even though EXAFS is a powerful method with a number of advantages, such as that no long-range order is necessary, all kinds of materials can be investigated, nondestructively. The analysis of EXAFS data is quite challenging, however, and effects such as structural disorder, if the sample is a mixture of components (not pure) or if the APNCs have several binding ligands, can distort the results. The use of l-DOS based on theoretical XANES calculations that can give information about electronic properties of APNCs is also challenging. In complement with XPS experiments, however, consistent answers can be found.
Thermodynamic studies of zippeite, a uranyl sulfate common in mine wastes

Abstract Zippeite is a potassium uranyl sulfate mineral that forms on uranium mine wastes and that may be important in nuclear waste disposal. Little is known about its thermodynamic properties. In this study, we synthesized zippeite, K3(H2O)3.3[(UO2)4(SO4)2O3(OH)], and measured its thermodynamic properties. The standard enthalpy of formation of zippeite from the elements, − 8655.97 ± 12.55 kJ/mol, was calculated from the measured enthalpy of dissolution in a high-temperature oxide melt solution calorimeter. Solubility measurements were conducted from both undersaturation and supersaturation in order to constrain the equilibrium state. Using the solubility product (Ksp) obtained from the solubility data, the standard Gibbs free energy of formation of zippeite at 298 K was calculated to be − 7783.44 ± 6.87 kJ/mol. This value, coupled with the standard enthalpy of formation value determined from the calorimetric data, was then used to calculate the standard entropy of formation, − 2926.49 ± 45.64 J/mol. Our studies yield the first complete set of thermodynamic properties of zippeite, and the results allow us to predict the conditions under which its formation is favorable relative to other uranyl minerals under a wide range of conditions of geologic and engineering interest.
The genus Nactus (Lacertilia: Gekkonidae): a phylogenetic analysis and description of two new species from the Papuan Region

Two new geckos from islands off the southeastern tip of New Guinea are not readily assignable to any currently defined genus but appear closely related to Nactus. The defining features of Nactus, however, have been uncertain because of variation among species assigned to this group, character convergence with other genera, and varying character emphases of different researchers. Moreover, relationships of Nactus to other gekkonine genera are uncertain because of homoplasy among the few characters used to infer higher-level relationships within Gekkoninae. I performed an analysis of phylogenetic relationships of my two new species to members of Nactus using a variety of other gekkonine and diplodactyline genera as outgroups. The results indicate the two new species are derived members of the genus Nactus that have undergone evolutionary reversal of some of the characters previously used to distinguish this genus. A further result of my analyses is that Nactus as currently conceived may prove paraphyletic or polyphyletic because its two most morphologically divergent species fail to cluster with the remaining members of this genus in all analyses. The two new species are herein described as Nactus sphaerodactylodes sp. nov. and Nactus acutus sp. nov. and may readily be distinguished from the other members of the genus by a variety of scalational features.
EVIDENCE OF LOWER-ATMOSPHERIC OZONE “SLOSHING” IN AN URBANIZED VALLEY

The objective of the research that is presented here was to reveal evidence of the complete diurnal process by which high concentrations of lower-atmospheric ozone are typically transported across the Phoenix (Arizona) Valley. The spatial and temporal patterns of diurnal ozone concentrations and the associated atmospheric flow patterns were examined on three spatial scales for a two-month period during summer 1998. On 11 study days marked by high ozone concentrations, ozone and atmospheric data on the micro and mesoscales suggest the dominant ozone transport mechanism to have been a mountain-valley thermal circulation. During daytime hours an apparent anabatic wind effectively transported high concentrations of ozone from an area of high ground traffic south of the urban center northeastward toward higher terrain. On 6 of the 11 high ozone days the temporal patterns of ozone concentration and atmospheric flow indicate the nighttime return of the same ozone from the higher terrain as a result of downslope ...
Diet assessment of the Atlantic Sea Nettle Chrysaora quinquecirrha in Barnegat Bay, New Jersey, using next-generation sequencing

Next-generation sequencing (NGS) methodologies have proven useful in deciphering the food items of generalist predators, but have yet to be applied to gelatinous animal gut and tentacle content. NGS can potentially supplement traditional methods of visual identification. Chrysaora quinquecirrha (Atlantic sea nettle) has progressively become more abundant in Mid-Atlantic United States' estuaries including Barnegat Bay (New Jersey), potentially having detrimental effects on both marine organisms and human enterprises. Full characterization of this predator's diet is essential for a comprehensive understanding of its impact on the food web and its management. Here, we tested the efficacy of NGS for prey item determination in the Atlantic sea nettle. We implemented a NGS 'shotgun' approach to randomly sequence DNA fragments isolated from gut lavages and gastric pouch/tentacle picks of eight and 84 sea nettles, respectively. These results were verified by visual identification and co-occurring plankton tows. Over 550 000 contigs were assembled from ~110 million paired-end reads. Of these, 100 contigs were confidently assigned to 23 different taxa, including soft-bodied organisms previously undocumented as prey species, including copepods, fish, ctenophores, anemones, amphipods, barnacles, shrimp, polychaete worms, flukes, flatworms, echinoderms, gastropods, bivalves and hemichordates. Our results not only indicate that a 'shotgun' NGS approach can supplement visual identification methods, but targeted enrichment of a specific amplicon/gene is not a prerequisite for identifying Atlantic sea nettle prey items.
Mechanochemistry of Physisorbed Molecules at Tribological Interfaces: Molecular Structure Dependence of Tribochemical Polymerization

Physisorbed molecules at a sliding solid interface could be activated by mechanical shear and react with each other to form polymeric products that are often called tribopolymers. The dependence of the tribopolymerization yield on the applied load and adsorbate molecular structure was studied to obtain mechanistic insights into mechanochemical reactions at a tribological interface of stainless steel. Three hydrocarbon precursors containing 10 carbon atoms—α-pinene (C10H16), pinane (C10H18), and n-decane (C10H22)—were chosen for this study. α-Pinene and pinane are bicyclic compounds with different ring strains. N-Decane was chosen as a reference molecule without any internal strain. By comparing the adsorption isotherm of these molecules and the total volume of tribopolymer products, the reaction yield was found to be proportional to the number of adsorbed molecules. An Arrhenius-type analysis of the applied load dependence of the tribopolymerization yield revealed how the critical activation volume (ΔV*) ...
A string-based cohesive zone model for interlaminar delamination

Abstract The objective of this paper is to develop a string-based cohesive zone model (CZM) for interlaminar delamination, whose associated cohesive elements behave reliably and consistently when deformed along complex separation paths and can display experimental critical energy release rate–mode mixture ratio relationships. Each cohesive element is idealized as a deformable string exhibiting path dependent damage behavior, and the thermodynamic equations are formulated in a generalized standard manner. A damage model having a path dependence function is developed. The rate form of the cohesive law is subsequently derived. The path dependence function is constructed such that each cohesive element can exhibit designated, possibly sophisticated mixed-mode behavior. The interface parameters associated with the present CZM are calibrated from experimental data. The present CZM is validated through simulating a series of flexural tests using Abaqus/Explicit. It is found to be capable of producing reliable simulation results. The interfacial strength is found to affect the predicted applied load–load point displacement curves. The present CZM may be amended to handle other types of fracture or interfacial debonding.
PaPar: A Parallel Data Partitioning Framework for Big Data Applications

Today, big data applications can generate largescale data sets at an unprecedented rate; and scientists have turned to parallel and distributed systems for data analysis. Although many big data processing systems provide advanced mechanisms to partition data and tackle the computational skew, it is difficult to efficiently implement skew-resistant mechanisms, because the runtime of different partitions not only depends on input data size but also algorithms that will be applied on data. As a result, many research efforts have been undertaken to explore user-defined partitioning methods for different types of applications and algorithms. However, manually writing application-specific partitioning methods requires significant coding effort, and finding the optimal data partitioning strategy is particularly challenging even for developers that have mastered sufficient application knowledge. In this paper, we propose PaPar, a Parallel data Partitioning framework for big data applications, to simplify the implementations of data partitioning algorithms. PaPar provides a set of computational operators and distribution strategies for programmers to describe desired data partitioning methods. Taking an input data configuration file and a workflow configuration file as the input, PaPar can automatically generate the parallel partitioning codes by formalizing the user-defined workflow as a sequence of key-value operations and matrixvector multiplications, and efficiently mapping to the parallel implementations with MPI and MapReduce. We apply our approach on two applications: muBLAST, a MPI implementation of BLAST algorithms for biological sequence search; and PowerLyra, a computation and partitioning method for skewed graphs. The experimental results show that compared to the partitioning methods of applications, the codes generated by PaPar can produce the same data partitions with comparable or less partitioning time.
Detection of early pancreatic ductal adenocarcinoma with thrombospondin-2 and CA19-9 blood markers

Markers are needed to facilitate early detection of pancreatic ductal adenocarcinoma (PDAC), which is often diagnosed too late for effective therapy. Starting with a PDAC cell reprogramming model that recapitulated the progression of human PDAC, we identified secreted proteins and tested a subset as potential markers of PDAC. We optimized an enzyme-linked immunosorbent assay (ELISA) using plasma samples from patients with various stages of PDAC, from individuals with benign pancreatic disease, and from healthy controls. A phase 1 discovery study (n = 20), a phase 2a validation study (n = 189), and a second phase 2b validation study (n = 537) revealed that concentrations of plasma thrombospondin-2 (THBS2) discriminated among all stages of PDAC consistently. The receiver operating characteristic (ROC) c-statistic was 0.76 in the phase 1 study, 0.84 in the phase 2a study, and 0.87 in the phase 2b study. The plasma concentration of THBS2 was able to discriminate resectable stage I cancer as readily as stage III/IV PDAC tumors. THBS2 plasma concentrations combined with those for CA19-9, a previously identified PDAC marker, yielded a c-statistic of 0.96 in the phase 2a study and 0.97 in the phase 2b study. THBS2 data improved the ability of CA19-9 to distinguish PDAC from pancreatitis. With a specificity of 98%, the combination of THBS2 and CA19-9 yielded a sensitivity of 87% for PDAC in the phase 2b study. A THBS2 and CA19-9 blood marker panel measured with a conventional ELISA may improve the detection of patients at high risk for PDAC.
Relationships between chemotherapy, chemotherapy dose intensity and outcomes of follicular lymphoma in the immunochemotherapy era: A report from the University of Iowa/Mayo Clinic Lymphoma Specialized Program of Research Excellence Molecular Epidemiology Resource

The optimal treatment of follicular lymphoma (FL) is not established. Rituximab's value potentially dilutes the impact of chemotherapy on FL. We reviewed 337 cases of FL treated initially with rituximab as monotherapy or with chemotherapy at the University of Iowa/Mayo Clinic from 2002 to 2009, investigating the association between chemotherapy delivery of cyclophosphamide or doxorubicin and survival. With median follow-up duration of 52.7 months, event-free survival (EFS) and overall survival (OS) were similar between the two groups, with a trend toward better EFS in the R-chemotherapy cohort (hazard ratio [HR]=1.24, p=0.28). In the R-chemotherapy group, increased total dose delivery and delivered dose intensity of doxorubicin were associated with improved EFS only in patients who did not receive R-maintenance (HR=0.81; p=0.02 and HR=0.94; p=0.04). Cyclophosphamide delivery was not associated with EFS. Thus, in the immunochemotherapy era, chemotherapy delivery strategy requires re-evaluation.
Interactions of branched-chain amino acids and lipids in metabolic disease

We seek to apply metabolomics and other “omics” tools for understanding of mechanisms contributing to pandemic metabolic diseases such as type 2 diabetes, obesity, and cardiovascular disease. We ha...
Design, modelling, and application of a low void-volume in situ diffuse reflectance spectroscopic reaction cell for transient catalytic studies

This paper describes a new low void-volume in situ reaction cell for use in diffuse reflectance spectroscopic studies. It was demonstrated by means of a residence time distribution analysis that the cell's average gas residence time was relatively small (∼1.3 s) and within the time scale of rapid scan spectra sampling. Such combination enabled the rigorous implementation of transient periodic techniques such as modulation excitation-phase sensitive detection-diffuse reflectance Fourier infrared spectroscopy (ME-PSD-DRIFTS), which allowed unique access to surface reaction intermediates in gas–solid reactions. Application of the new cell and ME-PSD-DRIFTS to the conversion of ethanol on γ-Al2O3 at 200 °C demonstrated the presence of likely surface intermediate species that conform with ethanol conversion to diethyl ether via a SN2 mechanism and the involvement of several alumina hydroxyl types as possible active sites.
Physician Sexual Assault: The Moral Imperative for Gender Equity in Medicine.

Prepare to cringe as you read this issue’s article entitled “Serious Ethical Violations in Medicine” by DuBois, Anderson, and colleagues (DuBois et al. 2019). In their analysis of 280 physician mis...
Reliability and accuracy of smartphones for paediatric infectious disease consultations for children with rash in the paediatric emergency department

Smartphones and associated messaging applications have become the most common means of communication among health care workers and the general population. The aim of this study was to evaluate the reliability and accuracy of smartphones for the diagnosis of rash in children admitted to emergency departments during the night shift. The images of the children who were admitted to the paediatric emergency department with rash were included in this study, and at least two images taken with smartphones by residents or paediatric infectious disease fellows were re-directed to the chief consultant of the Paediatric-Infectious Department via smartphone. Initial diagnosis by the consultant was recorded, and the patient’s physical examination was performed by another clinician on the first working day; diagnostic tests were planned by this clinician. The definitive diagnosis was recorded and compared with the initial diagnosis. Among the 194 patients, the most common final diagnoses were chickenpox (varicella-zoster infections) in 33 patients (17.0%) and skin infections (including impetigo, ecthyma, erysipelas and cellulitis) in 33 patients (17.0%). The initial diagnosis, which was performed via WhatsApp on a smartphone, was identical to the final diagnosis in 96.3% of the cases. Incompatible initial diagnoses included 4 measles cases, 1 staphylococcal scalded skin syndrome case, 1 cutaneous leishmaniasis case and 1 petechial rash case. Our study has shown that the use of a smartphone-based instant messaging application for transmitting images of paediatric rash is accurate and useful for diagnosis. However, physical examination and medical history are still the primary methods. Consultation via smartphones in emergency departments for paediatric rashes during nightshifts would help both clinicians and patients.