cssi/SciSciGPT-SciSciNet huggingface dataset:
Gene Expression Analysis Using Conventional and Imaging Methods

Understanding the intricacies of gene expression is important for unraveling the mechanisms of growth, development, and maintenance of normal cell metabolism. Recently developed techniques such as cDNA-microarray hybridization or high-throughput RNA sequencing provide overall snapshots of the entire transcriptome of a given sample and have greatly shaped the development of biomedical research since the late 1990s. With the availability of next-generation sequencing technologies, whole transcriptome analysis is quickly becoming affordable and common practice in biological research. Quantification of gene expression is critical to understand gene regulatory networks, interpret epigenetic gene regulation, identify noncoding regulatory RNAs, and pinpoint genes involved in disease states or disorders. However, understanding the variability of gene expression from cell-to-cell demands a set of complementary tools that can be used to characterize gene expression networks in single cells. In this chapter, we review the recent advances in probe design chemistry, developments in imaging, and the need for spatial and temporal single-molecule transcript quantification. Additionally, we discuss the applicability of novel nanoparticle-based approaches for imaging RNA dynamics and quantification in medicine and molecular biology.
Comparison of two atmospheric correction approaches applied to MODIS measurements over North American waters

Abstract Using in situ data of spectral remote sensing reflectance (Rrs, sr−1) collected over North American oceanic, coastal and estuarine waters between 2002 and 2016 (N = 942), we evaluate two atmospheric correction approaches applied to MODIS measurements. One is the POLYnomial based approach originally designed for MERIS (POLYMER) but adopted and implemented for MODIS, and the other is the traditional Gordon and Wang (1994b) near-infrared (NIR) approach with iteration to account for non-negligible NIR water-leaving radiance, which is currently embedded in the SeaWiFS Data Analysis System (SeaDAS) software package and used operationally by NASA for processing MODIS data (termed as NASA standard atmospheric correction or NSAC). The approaches are evaluated for both quality and quantity of their retrieved Rrs in the visible domain. The quality is gauged through three statistical measures between in situ and MODIS-retrieved Rrs: root mean square error (RMSE, sr−1), unbiased root mean square (uRMS), and mean bias (δ, sr−1). For common points where both approaches yield valid Rrs retrievals, POLYMER shows worse performance than NSAC for blue bands (
Myeloperoxidase loss protects against delayed cerebral injury after subarachnoid hemorrhage

Abstract Background Neutrophil infiltration into the central nervous system (CNS) after aneurysmal subarachnoid hemorrhage (SAH) is critical to the development of delayed cerebral injury (DCI). The goal of the present study is to characterize the neutrophil activity that leads to DCI. Methods We tested mice deficient in elastase, NADPH oxidase, or myeloperoxidase (MPO) in our SAH model for delayed spatial memory changes and vascular constriction associated with DCI. Because the MPO mouse showed no DCI, we focused on the MPO null mice, including experiments to reconstitute the MPO effect by injection of active MPO and its substrate, H2O2. Flow cytometry and immunohistochemistry were used to determine the temporal and spatial location of neutrophils and glial cells in the CNS after SAH in WT and MPO null mice. Results Following SAH, neutrophils infiltrate the outer meninges from outside the CNS in a delayed fashion. Mice with functional deletion of the neutrophil effector molecule myeloperoxidase (MPO KO) do not develop DCI. Re-introduction of biologically active MPO to the meninges, i.e. CSF, of MPO KO mice at the time of the hemorrhage restores the spatial memory deficit seen in DCI. However, addition of active MPO to the CSF of wildtype mice (WT) without hemorrhage does not lead to DCI, suggesting that blood components and MPO are necessary to cause DCI in our model. The localization of neutrophils, exclusively in the meninges, suggests that their effect on spatial memory goes through intermediate cells (presumably glia). Astrocyte reactivity increases in WT after SAH but not in MPO KO mice, suggesting that astrocytes mediate the effects of neutrophil-derived MPO on neurons in the brain parenchyma after SAH. Conclusions These results demonstrate that neutrophils can modulate cognition from the meninges, and that immune cell reactivity in the meninges can modulate spatial memory through indirect effects on neurons.
Some limit results in estimation of proportion based on group testing

Group testing that tests groups with k experimental units instead of individuals has a long history and is very useful for estimating small proportion p under certain conditions. There are two sampling schemes for implementing group testing, one is Binomial sampling in which the number of groups n is predetermined, and another one is negative binomial sampling where the total number n of groups with a trait is predetermined. Many estimators including both the frequentist and Bayesian estimator have been proposed. The performance of all these estimators certainly depends on n and k. For the Bayesian estimators it also depends on the hyper-parameter $$\beta $$ in the prior distribution $$Beta(1, \beta )$$ of the proportion p. The present article studies the limits of all these estimators when n, or k, or $$\beta $$ goes to infinity. The obtained results may be helpful with selecting n, k, and $$\beta $$ .
Cost Comparison of Left Ventricular Assist Device versus Intra Aortic Balloon Pump as Bridge to Heart Transplant

Background Optimal device for bridge to heart transplant (BTT) is unknown. We compared costs and complications associated with left ventricular assist device (LVAD) versus intra-aortic balloon pump (IABP) as primary BTT strategies, as well as outcomes one-year post heart transplant (HTx). Methods 11 IABP patients were matched with 11 LVAD patients by age ± 5 years, body mass index (BMI) ± 5 k g/m², and exact blood type. The mean age was 54±9 years, 18% were female, and mean BMI was 27±4 kg/m² (Table 1). Two IABP (18.2%) patients crossed over to LVAD or ECMO. Results Average cost of index hospitalization did not reach statistical significance between LVAD and IABP patients based on primary device modality (median[IQR]: 183[175-221] vs 241[218-261]) (p=0.065). Total BTT costs were higher for LVAD patients (449[379-657] vs 244[225-348]) (p=0.012) (see Figure 1). Complications are listed in Table 2. Eight (73%) LVAD and all IABP patients were alive at one year post-HTx (p=0.25). Other one-year outcomes from time of HTx were similar (Table 3). Conclusion BTT with LVAD compared to IABP is associated with higher costs. For patients who can be stabilized on IABP, IABP is a cost-effective method.
HIV care cascade before and after hospitalization: impact of a multidisciplinary inpatient team in the US South

Hospitalization represents a unique opportunity to re-engage out-of-care individuals, improve HIV outcomes and reduce health disparities. Electronic health records of HIV-positive individuals hospi...
Why Research on Lyme Disease and Ixodes scapularis Needs Wildlife Ecology without Taxonomic Bias: A Review

Ixodes ticks are obligate parasites that show host preferences and differentiation during each of their 3 active life stages and may obtain or transmit pathogens during feeding that pose threats to human health. These ticks are responsible for the transmission of Borrelia burgdorferi, causative agent of Lyme Disease. Historically, ticks and B. burgdoferi have been well studied due to this human threat. However, wildlife hosts other than mice or deer that may serve as reservoirs for tick species are often overlooked as a part of this web. In this study, we surveyed 40,000+ manuscripts and identified those that considered wildlife hosts when studying Ixodes scapularis(Blacklegged Tick). We found that there appears to be a taxonomic bias in research on wildlife hosts and that this may be contributing to a continued lack of knowledge about potential transmission and management of Blacklegged Ticks or Lyme Disease. Collectively, these findings suggest that more information is needed on wildlife hosts and tick-host ecology, particularly that of birds, meso-mammals and reptiles. Finally, we propose a list of potential research questions that could help further elucidate the importance of wildlife and tick-host ecology.
Limits to flow detection in pulsed gradient spin echo NMR

Velocity detection with single pulsed gradient spin echo (PGSE) NMR is known to be limited by diffusion smearing the phase coherence and obscuring dispersive attenuation. We present an equation for the lowest detectable velocity with phase contrast velocimetry which incorporates the signal-to-noise ratio. We show how to best sample q-space when approaching this limit. We confirm that the apparent diffusion/dispersion coefficient can be used to infer fluid velocity for Peclet number Pe > 1. When measuring flow in biological systems we determined that with realistic experimental protocols the limits are roughly 1 {micro}m/s for velocimetry and 300 {micro}m/s for diffusometry.
Case 10-2020: An 83-Year-Old Man with Pancytopenia and Acute Renal Failure

A Man with Pancytopenia and Acute Renal Failure An 83-year-old man presented with pancytopenia and acute renal failure. The haptoglobin level was normal, but levels of d-dimer and lactate dehydroge...
Open Longitudinal Pancreaticojejunostomy

This chapter discusses technical aspects of open longitudinal pancreaticojejunostomy, including instrumentation and equipment, patient positioning, and surgical steps. The authors also offer pearls and pitfalls.
Vitamin D and sleep in children.

Study Objectives:The impact of vitamin D on human health including sleep has been well described in adults. Its deficiency has been associated with multiple sleep disorders such as decrease in slee...
Natural and anthropogenic processes affecting radon releases during mining and early stage reclamation activities, Pinenut uranium mine, Arizona, USA.

Abstract Radon (Rnair) was monitored in open air in publicly accessible areas surrounding the Pinenut uranium (U) mine during mining and reclamation activities in 2015–16 to address concerns about mining related effects to areas surrounding Grand Canyon National Park (GCNP) in Arizona, USA. During July 2015, Rnair concentrations associated with the ore storage pile monitoring site were larger than those at the mine vent monitoring site and likely resulted from the relatively large amount of ore stored on site during this period. Higher wind velocities at the ore pile monitoring site generally resulted in lower Rnair concentrations; however, wind velocity did not appear to be an important factor in controlling Rnair concentrations at the mine vent monitoring site. Physical disturbances of the ore pile by heavy equipment did not coincide with elevated Rnair concentrations at the ore storage pile or mine vent monitoring sites. The relative size of the ore storage pile showed a positive trend with the daily mean Rnair concentration measured at the ore pile monitoring site. Principal component analysis (PCA) was applied to the ore pile and mine vent multivariate data sets for simultaneous comparison of all measured variables during 230 days of the study period. A significant positive coefficient for Rnair was associated with a significant negative coefficient for wind speed for principal component (PC) 2ore pile. Significant, positive PC2mine vent coefficients included Rnair, wind direction, and relative ore pile size indicating that Rnair variations at the mine vent monitoring site may be affected by Rn sourced from the ore pile. The ore pile is located about 200 m south of the mine vent Rn monitor with the prevalent wind direction coming from the south. All data generated during the field study and laboratory verification tests were published by Naftz et al. (2018) and are available online at: https://doi.org/10.5066/F79Z946T .
Feasibility of Implementing Opioid Stewardship Recommendations for Sinonasal Surgery.

ObjectiveThe objective of our study was to review the current literature pertaining to perioperative opioids in sinus surgery and to determine the effects of implementing opioid stewardship recomme...
Deformable Image Registration with a Scale-adaptive Convolutional Neural Network

Multi-resolution hierarchical strategy is typically used in conventional optimization-based image registration to address large deformation and improve the chance of a good local minimum. A rough concept of the scale is captured in deep networks by the reception field of kernels, and it has been realized to be both desirable and challenging to capture convolutions of different scales simultaneously in registration networks. In this study, we propose an image registration network that is conscious of and self-adaptive to deformation of various scales. Dilated inception modules (DIMs) are proposed to incorporate receptive fields of different sizes in a computationally efficient way. Scale adaptive modules (SAMs) are proposed to guide and adjust shallow features using convolutional kernels with spatially adaptive dilation rate learned from deep features. DIMs and SAMs are integrated into the registration network which takes a U-net structure. The network is trained in an unsupervised setting and completes registration with a single evaluation run. Experiment with cardiac MRIs showed that the adaptive dilation rate in SAM corresponded well to the deformation scale. Evaluated with left ventricle segmentation, our method achieved a dice of $(0.93\pm 0.02)$, significantly better than SimpleElastix and networks without DIM or SAM. Assessment with respect to average surface distance was less than 2 millimeters (1.6 pixels), comparable to the best-performing SimpleElastix without statistical significance. Experiment with synthetic data also demonstrated the effectiveness of DIMs and SAMs, which leaded to a significant reduction in target registration error based on dense deformation field. The average registration time was 4 milliseconds for 2D image with size $256\times 256$.
Molecular Motions and Solvent Stabilization of Charges

The solution phase properties of ionic molecules are an important area of chemistry because of the common occurrence of charged species in reaction pathways and the large interactions of solvent with ionic molecules. In this work we report studies of rotational relaxation of a single ionic molecule in a variety of solvent environments.
Electrochemical study of the dissolution of oxide films grown on type 316L stainless steel in molten fluoride salt

Abstract The corrosion behavior of oxide films grown on Type 316L stainless steel (SS) in molten FLiNaK (LiF-NaF-KF: 46.5−11.5−42 mol.%) salt was investigated. The results show that the oxide film formed on Type 316L SS is unstable and can only temporarily protect materials from corrosion in molten FLiNaK salt. Based on the electrochemical impedance spectroscopy, the oxide dissolution rate is calculated to be 0.85 nm/h at 700 °C in molten FLiNaK salt. After the oxide film dissolved, Cr and Fe are selective dealloyed from the steel, leading to intergranular corrosion of Type 316L SS in molten fluoride salt.
Small nucleolar RNAs in plasma and their discriminatory power as diagnostic biomarkers of Alzheimer's disease

AO_SCPLOWBSTRACTC_SCPLOWThe clinical diagnosis of Alzheimers disease, at its early stage, remains a difficult task. Advanced imaging technologies and laboratory assays to detect A{beta} peptides A{beta}42 and A{beta}40, total and phosphorylated tau in CSF provide a set of biomarkers of developing AD brain pathology and facilitate the diagnostic process. The search for biofluid biomarkers, other than in CSF, and the development of biomarker assays have accelerated significantly and now represent the fastest-growing field in AD research. The goal of this study was to determine the differential enrichment of noncoding RNAs (ncRNAs) in plasma-derived extracellular vesicles (EV) of AD patients and Cognitively Normal controls (NC). Using RNA-seq, we profiled four significant classes of ncRNAs: miRNAs, snoRNAs, tRNAs, and piRNAs. We report a significant enrichment of SNORDs - a group of snoRNAs, in AD samples compared to NC. To verify the differential enrichment of two clusters of SNORDs - SNORD115 and SNORD116, localized on human chromosome 15q11-q13, we used plasma samples of an independent group of AD patients and NC. We applied ddPCR technique and identified SNORD115 and SNORD116 with a high discriminatory power to differentiate AD samples from NC. The results of our study present evidence that AD is associated with changes in the enrichment of SNORDs, transcribed from imprinted genomic loci, in plasma EV and provide a rationale to further explore the validity of those SNORDs as plasma biomarkers of AD.
Model Predictive Control of Material Volumes with Application to Vortical Structures

In this paper, a model predictive control algorithm for selectively steering material volumes in a boundary layer is proposed. Using direct numerical simulations of a laminar boundary layer with a ...
Perilymphatic fistula

A perilymph fistula is an abnormal connection between the inner and middle ear that allows escape of perilymph fluid into the middle ear compartment. The clinical symptomatology that follows leakage of fluid is by and large indistinguishable from a number of other pathologies that affect inner ear function. Definite diagnostic proof of a perilymph fistula remains elusive, and methods of diagnosis remain controversial. Traumatic tears in the oval or round windows remain a major cause of perilymph fistula, yet an index of suspicion in traumatic brain injury frequently remains low. The diagnosis of perilymph fistula must always be considered in the appropriate clinical setting of head trauma, barotrauma, and in patients with unresolved and undiagnosed episodes of recurrent vertigo or hearing loss. Surgical treament with patching of oval and round windows remains the mainstay of therapy for this condition.
Case-sensitive plural suppletion in Barguzin Buryat: On case containment, suppletion typology, and competition in morphology

This paper examines plural suppletion in the Barguzin dialect of Buryat (Mongolic, Russia), which occurs only in accusative and genitive noun phrases. The restricted distribution of this process, specifically its absence in oblique cases, is significant for recent research on the typology of suppletion and the feature structure of case. For much work in this vein, this plural suppletion would qualify as having an ‘ABA’ pattern, which is predicted to be unattested. I argue that the suppletive plural morpheme in question is a portmanteau whose morphological requirements cause it to conflict, for independent reasons, with the realization of oblique noun phrases. Consequently, I argue that its distribution does not falsify the theories that normally ban ABA patterns, but rather instantiates a principled exception to them which sharpens our understanding of them.
A multispecies turbulence model for the mixing and de-mixing of miscible fluids

A de-mix capable model for turbulence in compressible, variable density flows is proposed. The model is based on the Besnard-Harlow-Rauenzahn (BHR) family of models (Besnard D, Harlow F, Rauenzahn ...
Use of a Rubric to Improve the Quality of Internal Medicine Resident Event Reporting.

Introduction As frontline providers, residents report patient safety events and provide crucial safety feedback. Specific ACGME and AAMC requirements for graduating residents include active partici...
Extreme Weather Events and Interconnected Infrastructures: Toward More Comprehensive Climate Change Planning

The President's Climate Change Action Plan calls for the development of better science, data, and tools for climate preparedness. Many of the current questions about preparedness for extreme weathe...
Bite Mark Analysis

Courts have admitted bite mark comparison evidence in homicide, rape, and child abuse cases. By the 1980s, the technique had gained widespread judicial acceptance. Hundreds of cases have admitted this type of evidence, and no reported case has rejected it. Moreover, some courts speak of bite mark comparison as a 'science.' Indeed, its acceptance is so well-established that several courts have taken judicial notice of its reliability, implying that the validity of the technique is not subject to reasonable dispute. Yet, the scientific foundations for bite mark comparisons has never been demonstrated. Such basic issues as the uniqueness of the human dentition have not been established. Moreover, there is no agreement concerning the accuracy of these comparisons or about the best analytical procedure for making this determination. Recent DNA exonerations of defendants convicted based on bite mark analysis has now undermined the legal status of this method of proof.
Effect of Drugs upon Axoplasmic Transport

Publisher Summary This chapter discusses the effect of drugs upon axoplasmic transport. Axoplasmic transport is a neural activity of ever-increasing interest to the biochemist and physiologist. To understand the functions of the transported molecules and the manner in which they interact with the axon and synapse, employ agents that disrupt transport shall have to be employed. Several classes of such drugs are now available: inhibitors of karyokinesis, such as colchicine; antimetabolites, such as dinitrophenol; and important but poorly studied compounds, such as the neuropathogens. New types of compounds, such as the methoxylated phenalkylamines, are becoming available. Agents about which much is now known suggest that transported proteins are synthesized upon ribosomes using messenger RNA, which is, in turn, coded from DNA. Transport requires the use of metabolic energy, probably derived from carbohydrates through respiration. The act of transport involves intra-axonal filamentous structures, of which the microtubules and microfilaments are most strongly implicated.
Cryo‐hydrologic warming: A potential mechanism for rapid thermal response of ice sheets

[1] Cryo-Hydrologic (CH) warming is proposed as a potential mechanism for rapid thermal response of glaciers and ice sheets to climate warming. We present a simple parameterization to incorporate CH warming in thermal models of ice sheets using a dual-continuum concept, which treats ice and the cryo-hydrologic system (CHS) as overlapping continua with heat exchange between them. The presence of liquid water in the CHS due to surface melt leads to warming of the ice. The magnitude and time-scale of CH warming is controlled by the average spacing between elements of the CHS, which is often of the order of just 10's of meters. The corresponding time-scale of thermal response is of the order of years-decades, in contrast to conventional estimates of thermal response time-scales based on vertical conduction through ice (∼102–3 m thick), which are of the order of centuries to millennia. We show that CH warming is already occurring along the west coast of Greenland. Increased temperatures resulting from CH warming will reduce ice viscosity and thus contribute to faster ice flow.
A new metric for assessing quality in advanced graduate courses in computer science and engineering

In the graduate schools across the US, the teaching of graduate courses continues to constitute a significant component of graduate education. This paper presents a philosophy that underlies the design of a few advanced graduate courses at Arizona State University in the sub-disciplines of hardware description languages, communications networks, computer-aided design of digital systems, distributed systems, distributed algorithms, and modeling and simulation. From the philosophy, a new metric emerges-the extent and significance of the knowledge "discovered" by the students, towards evaluating the quality of such courses. Discovery refers to the knowledge that is brought out into the open, through logical reasoning from the first principles, by the student for himself/herself. It is significant in that it becomes an integral part of the individual who not only gains invaluable insight and confidence in the subject matter but can improvise, reason, and apply it to other areas in creative ways. The paper illustrates the application of the metric through a number of actual cases encountered during teaching at ASU. It also presents a list of the desirable attributes of the underlying educational environment to ensure success in the design and delivery of such courses.
Hemoglobin synthesis during amphibian metamorphosis. II. Synthesis of adult hemoglobin following thyroxine administration.

Abstract Hemoglobin synthesized in vitro by red blood cells of thyroxine-treated Rana catesbeiana tadpoles is shown to be identical to adult frog hemoglobin by Sephadex gel filtration, by polyacrylamide gel electrophoresis of hemoglobin and of aminoethylated globin chains, and by fingerprinting of tryptic digests. The cells responsible for the synthesis of the adult hemoglobin were identified by radioautography and could be distinguished from the red cells of non-metamorphosing tadpoles by their rounder shape, relatively larger nuclei and lower content of hemoglobin. Polyacrylamide gel electrophoresis of hemoglobin and globin polypeptide chains was also used to determine the stage at which a switch in hemoglobin synthesis occurred during natural metamorphosis.
Human Lens β-Crystallin Solubility

The human lens is composed primarily of water and proteins called crystallins. Insolubility of these crystallins is correlated with aging and cataractogenesis. The α-crystallins have chaperone-like activity in maintaining the solubility of denatured β- and γ-crystallins. One established test of this chaperone activity is the ability of α-crystallin to prevent thermal destabilization of β-crystallins. Several studies have addressed the effects of structural modifications of α-crystallin on chaperone activity, but little is known about the solubilities of the various β-crystallins or the effects of post-translational modifications. Understanding the solubilities of different forms of β-crystallins is important to elucidating the mechanism of chaperone activity. In this study, the solubilities of β-crystallins were examined. The β-crystallins included the gene products of βB2, βA1/A3, βA4, and βB1 as well as forms modified in vivo. Analysis of the β-crystallins by high performance liquid chromatography and mass spectrometry before and after heating revealed large differences in the relative solubilities of the β-crystallins. These results demonstrate a decreased solubility of specific β-crystallins and post-translational modifications that may play a role in the crystallin insolubility associated with aging and cataract.
Rebel Governance and Civilian Abuse: Comparing Liberia's Rebels Using Satellite Data

Rebel groups exhibit signicant variation in their treatment of civilians, with profound humanitarian consequences. This paper proposes a new theory of rebel group behavior based on resources and delegation within rebel organizations. Rebel leaders have incentives to maintain order in their territories but are constrained in their ability to control group members. Leaders establish control through spot payments and promises of future rewards to top commanders. The leader’s ability to oer these incentives is determined by the group’s partnerships with external patrons. The theory’s implications are examined through a spatial analysis of Liberia’s civil war using an original dataset derived through remote sensing methods.
Real-time neural networks: conjunctoid parallel implementation

Conjunctoids are model-based neural networks for categorical data, having features that include: generality, with special cases ranging from simple perceptron-like linear versions to full-blown versions that account for all possible associations among external variables; continuous learning and performance, with provisions for optimal updating as each new datum is received, based on Bayes decision theory; and separable learning as well as performance formulas, with provisions for breaking down necessary global computations into parallel components. In the paper, a simple PC implementation is described for a full-blown conjunctoid model on a small-scale setting. A design and implementation of the model on an NCUBE parallel platform and on a special purpose parallel platform are also described. >
Phenotypic Variation Is Almost Entirely Independent of the Host-Pathogen Relationship in Clinical Isolates of S. aureus.

Background A key feature of Staphylococcus aureus biology is its ability to switch from an apparently benign colonizer of ~30% of the population to a cutaneous pathogen, to a deadly invasive pathogen. Little is known about the mechanisms driving this transition or the propensity of different S. aureus strains to engender different types of host-pathogen interactions. At the same time, significant weight has been given to the role of specific in vitro phenotypes in S. aureus virulence. Biofilm formation, hemolysis and pigment formation have all been associated with virulence in mice. Design To determine if there is a correlation between in vitro phenotype and the three types of host-pathogen relationships commonly exhibited by S. aureus in the context of its natural human host, we assayed 300 clinical isolates for phenotypes implicated in virulence including hemolysis, sensitivity to autolysis, and biofilm formation. For comparative purposes, we also assayed phenotype in 9 domesticated S. aureus strains routinely used for analysis of virulence determinants in laboratory settings. Results Strikingly, the clinical strains exhibited significant phenotypic uniformity in each of the assays evaluated in this study. One exception was a small, but significant, correlation between an increased propensity for biofilm formation and isolation from skin and soft tissue infections (SSTIs). In contrast, we observed a high degree of phenotypic variation between common laboratory strains that exhibit virulence in mouse models. These data suggest the existence of significant evolutionary pressure on the S. aureus genome and highlight a role for host factors as a strong determinant of the host-pathogen relationship. In addition, the high degree of variation between laboratory strains emphasizes the need for caution when applying data obtained in one lab strain to the analysis of another.
Science Is the First Step to Siting Nuclear Waste Repositories

As Shaw [2014] notes, U.S. research on shale as a repository host was halted before expending anything close to the effort devoted to studying crystalline rock, salt, and—most notably—tuff at Yucca Mountain. The new political reality regarding Yucca Mountain may allow reconsideration of the decision to abandon research on shale as a repository host.
Prospective elementary teachers’ responses to unanticipated incorrect solutions to problem-solving tasks

Eliciting and responding to student thinking are high-leverage practices that have powerful implications for student learning. However, they are difficult to enact effectively, particularly for novices, and more research is needed to understand how teacher education can support teachers in developing these skills. This study examined ways prospective elementary teachers (PSTs) responded to unanticipated incorrect student solutions to high-demand problem-solving tasks and how their responses changed over a 6-week field experience embedded in a practiced-based mathematics methods course. Data were collected in 6 weekly cycles of planning (written plans), enactment (video of problem-solving sessions with students), and reflection (written reflections on video). Problem-solving task implementations were analyzed using cognitive demand and math-talk frameworks. Of the three collaborating PST groups, two groups improved at responding to unanticipated incorrect solutions, but these two groups also developed a tendency to shut down anticipated solutions. The third group showed no patterns in their responses to unanticipated incorrect solutions, but did maintain the cognitive demand when responding to anticipated solutions. I present a case of one group of collaborating PSTs who made improvements in responding to unanticipated incorrect solutions in terms of the pedagogical moves they employed, cognitive demand associated with their responses, and how their responses changed over time. Implications for teacher education are discussed.
10 Reaction mechanisms

This chapter provides an overview of the 2002 literature pertaining to the mechanism and kinetics of reactions involving neutral free radicals and radical ions in solution. This overview begins by highlighting significant contributions to our understanding of fundamental classes of reactions: atom abstraction, addition, and fragmentation. Afterwards, rearrangement reactions, which are generally unimolecular variants of these fundamental classes, are examined. Next, the chemistry of radical ions is explored in a section dealing with reactions initiated by single electron transfer. This section deals with reactions which do not readily fall under one of the aforementioned classifications (e.g., pericyclic reactions initiated by single electron transfer). Short sections dealing with radical reactions in biological systems, and new methods of radical generation close the chapter. Interesting examples of the use of radical reactions in synthesis are interspersed throughout this report, however, the coverage of this important area is far from exhaustive.
Quantifying brain shift during neurosurgery using spatially tracked ultrasound

Brain shift during neurosurgery currently limits the effectiveness of stereotactic guidance systems that rely on preoperative image modalities like magnetic resonance (MR). The authors propose a process for quantifying intraoperative brain shift using spatially-tracked freehand intraoperative ultrasound (iUS). First, one segments a distinct feature from the preoperative MR (tumor, ventricle, cyst, or falx) and extracts a faceted surface using the marching cubes algorithm. Planar contours are then semi-automatically segmented from two sets of iUS b-planes obtained (a) prior to the dural opening and (b) after the dural opening. These two sets of contours are reconstructed in the reference frame of the MR, composing two distinct sparsely-sampled surface descriptions of the same feature segmented from MR. Using the Iterative Closest Point (ICP) algorithm one obtains discrete estimates of the feature deformation performing point-to-surface matching. Vector subtraction of the matched points then can be used as sparse deformation data inputs for inverse biomechanical brain tissue models. The results of these simulations are then used to modify the pre-operative MR to account for intraoperative changes. The proposed process has undergone preliminary evaluations in a phantom study and was applied to data from two clinical cases. In the phantom study, the process recovered controlled deformations with an RMS error of 1.1 mm. These results also suggest that clinical accuracy would be on the order of 1-2mm. This finding is consistent with prior work by the Dartmouth Image-Guided Neurosurgery (IGNS) group. In the clinical cases, the deformations obtained were used to produce qualitatively reasonable updated guidance volumes.
Rapid onset of mate quality assessment via chemical signals in a woodland salamander (Plethodon cinereus)

In the competition to acquire mates, environmental factors can be important in determining the relative quality of an individual. These aspects of quality are often conveyed through signals used for mate assessment by the most energetically invested sex. In red-backed salamanders, Plethodon cinereus, chemical signals communicate a surprising amount of information, much of which is dependent on the current condition of the sender. One such condition-dependent aspect of information conveyed via chemicals is the quality of the sender’s diet, but it is unclear as to whether this information is actively advertised by the sender (i.e., a signal) or simply inferred from food-derived odors (i.e., a cue). The amount of time on different diets required for changes in signaling is also unknown. I examined how quickly gravid female salamanders could detect a difference between the scents of males on high- vs. low-quality diets without fecal cues. The amount of protein present in two known signaling glands (the mental and postcloacal glands) was also measured after experimental feeding. Gravid females were able to infer the differences in male diet quality after only 1 week. Females also responded to the male scents more quickly after differential feeding had begun. High-quality males had significantly more protein present in both signaling glands than low-quality males. This scenario highlights the ongoing interplay between the quality of an individual and its environment, with males actually advertising the status of this relationship as an honest signal for mate assessment.
High Rate Dry Etching of GaN, AIN and InN in ECR Cl2/CH4/H2/Ar Plasmas

Etch rates for binary nitrides in ECR Cl2/CH4/H2/Ar are reported as a function of temperature, rf-bias, microwave power, pressure and relative gas proportions. GaN etch rates remain relatively constant from 30 to 125 °C and then increase to a maximum of 2340 A-min−1 at 170 °C. The AIN etch rate decreases throughout the temperature range studied with a maximum of 960 A-min−1 at 30 °C. When CH4 is removed from the plasma chemistry, the GaN and InN etch rates are slightly lower, with less dramatic changes with temperature. The surface composition of the III–V nitrides remains unchanged over the temperatures studied. The GaN and InN rates increase significantly with rf power, and the fastest rates for all three binaries are obtained at 2 mTorr. Surface morphology is smooth for GaN over a wide range of conditions, whereas InN surfaces are more sensitive to plasma parameters.
Primary Pulmonary Botryomycosis: Case Report and Review

Botryomycosis is an uncommon bacterial disease characterized by the microscopic formation of eosinophilic granules that resemble those of infection by Actinomyces species. The diagnosis of botryomycosis can be made when microscopic inspection and culture of the granules reveal gram-positive cocci or gram-negative bacilli. Botryomycosis is caused by common bacterial pathogens including Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa, yet the host and microbial factors that contribute to the pathobiology remain unknown. Pulmonary botryomycosis can resemble actinomycosis, tuberculosis, or invasive carcinoma by causing a mass lesion with constitutional symptoms. Radiographically, it invades bone and disrupts tissue planes. Successful treatment often requires a combination of both surgical debridement and long-term antimicrobial therapy. We report a case of primary pulmonary botryomycosis and review the literature on this unusual infectious process.
On 2-transitive collineation groups of finite projective spaces

A collineation group Γ ofPG(d, q), d ≧ 3, which is transitive on lines is shown to be 2-transitive on points unlessd=4,q=2 and |Γ|=31·5.
Common cause: Taking care of print collections

Drawing from information gathered by Center for Research Libraries (CRL) and published by Council on Library and Information Resources (CLIR) in the report Developing Print Repositories: Models for Shared Preservation and Access, this talk sets the context for the day's discussions by focusing on the challenges to building and sustaining these types of print repositories. Discussion will focus on identifying key elements of the infrastructure needed to support such repositories; economic incentives to cooperate in supporting these repositories; and the roles and responsibilities of those who provide such services and those who benefit from them.
Ethosuximide reduces electrographical and behavioral correlates of alcohol withdrawal seizure in DBA/2J mice

Chronic alcohol abuse depresses the nervous system and, upon cessation, rebound hyperexcitability can result in withdrawal seizure. Withdrawal symptoms, including seizures, may drive individuals to relapse, thus representing a significant barrier to recovery. Our lab previously identified an upregulation of the thalamic T-type calcium (T channel) isoform CaV3.2 as a potential contributor to the generation and propagation of seizures in a model of withdrawal. In the present study, we examined whether ethosuximide (ETX), a T-channel antagonist, could decrease the severity of ethanol withdrawal seizures by evaluating electrographical and behavioral correlates of seizure activity. DBA/2J mice were exposed to an intermittent ethanol exposure paradigm. Mice were treated with saline or ETX in each withdrawal period, and cortical EEG activity was recorded to determine seizure severity. We observed a progression in seizure activity with each successive withdrawal period. Treatment with ETX reduced ethanol withdrawal-induced spike and wave discharges (SWDs), in terms of absolute number, duration of events, and contribution to EEG power in the 6-10 Hz frequency range. We also evaluated the effects of ETX on handling-induced convulsions. Overall, we observed a decrease in handling-induced convulsion severity in mice treated with ETX. Our findings suggest that ETX may be a useful pharmacological agent for studies of alcohol withdrawal and treatment of resulting seizures.
STARview: a multiresolution time series data visualizer

We present an application case study for visualizing large data sets of time series spatial data. Our application is built on a flexible, object oriented framework that supports the visualization of dynamic internal wave propagation in the earth's tropopause. Our data model uses a multiresolution hierarchy that integrates spatial and temporal components. The data also includes error information at each level of the hierarchy. The application provides the scientist with tools necessary to examine, query, and interact with visualizations of data of interest.
Systematic Control of Particle Size in Rapid Open-Vessel Microwave Synthesis of K-OMS-2 Nanofibers

Multigram quantities of manganese oxide (K-OMS-2) nanomaterials in the size range of 4−20 nm and with very high surface areas up to 227 m2/g were produced rapidly via microwave-reflux route with use of mixed aqueous and nonaqueous solvents. The formation process, particle size, crystallite size, crystal structure, and properties of these nanomaterials were characterized by X-ray diffraction, scanning electron microscopy (SEM), transmission electron microscopy (TEM), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), infrared spectroscopy (FT-IR), Raman spectroscopy, and nitrogen adsorption−desorption. The OMS-2 nanofiber diameter was systematically controlled by varying the concentration or type of the cosolvent. Catalytic studies of these K-OMS-2 nanomaterials for oxidation of anisyl alcohol were performed. These nanomaterials show excellent catalytic activity when compared with conventionally prepared bulk OMS-2 catalysts.
Private Sector Participation and Health System Performance in Sub-Saharan Africa

Researchers analyzed data on child and maternal health care use from 34 sub-Saharan African countries to examine the association between the degree of private sector participation in the health care system and outcomes related to access and equity.
Commentary: real‐world triple therapy experience treating hepatitis C virus – authors' reply

We thank Heron and colleagues for their interest in our report 2 and agree that the cost-effectiveness of this therapy is called into question by the number of patients who are unable to complete treatment and successfully achieve sustained virological response. We are analysing the cost-effectiveness of this regimen using real-world data. Ribavirin dose reduction during treatment was not recorded in more than 50% of our patients. As decisions on adverse event management were at the discretion of individual clinicians, anaemia management varied. Several patients received erythropoietin (EPO) therapy prior to ribavirin dose reduction, and some had signs of severe anaemia at the first or second visit and required blood transfusion before dose reduction might have been possible. Thus, great importance must be placed on careful patient monitoring when using these medications. With some exceptions, ribavirin dose was reduced when patients had haemoglobin levels of 10 g/dL or less. If haemoglobin levels fell to below 8.5 g/dL, patients were given EPO. As mentioned in our report, only 16% of our patients had IL28b testing; the results of this test were not used to reach a decision on initiation of therapy. We did not collect hepatitis C virus genotype-1 subtype data, but future studies will certainly examine the effect that genotype and subtype may have on the occurrence of adverse events.
Comparison of eleven soil termiticides against the Formosan subterranean termite and eastern subterranean termite (Isoptera: Rhinotermitidae.

Toxicities of 11 topically applied termiticides to the Formosan subterranean termite, Coptotermes formosanus Shiraki, and the eastern subterranean termite, Reticulitermes flavipes (Kollar) were determined. At LD50, deltamethrin was most toxic (0.12 and 0.01 μg/g for C. Formosan us and R. fiavipes , respectively), while chlordane was least toxic (LD50:45.34 and 20.10 μg/g, respectively). R. flavipes was more susceptible to all termiticides than C. formosanus . The relative susceptibility of the two termite species ( C. formosanus LD50÷ R. fiavipes LD50) ranged from 2.0 (chlorpyrifos) to 12.9 (bifenthrin). In a tunneling test in which termites were given a choice of penetrating or avoiding treated soil, all nine pyrethroids tested were repellent at sublethal doses. At appropriate concentrations, termites did not penetrate soil treated with pyrethroids and did not contact the toxicant. Significant mortality was mostly observed as termites tunneled through deposits of chlordane and chlorpyrifos and were killed by constant exposure. Soil treated with chlordane was most vulnerable to termite tunneling activity. Both termite species penetrated the 5 cm soil treated with 10 ppm of chlordane. Tunneling was inhibited with both species in soil treated with 1 ppm permethrin, while deltamethrin and cyhalothrin totally stopped tunneling by R. fiavipes at the concentrations as low as 0.4-0.8 ppm.
Performance estimation of a manufacturing cell using rotation scheduling

We propose an approximation approach for estimating the system performance of a manufacturing cell using a Rotation rule for production sequencing. The method has two steps. We first decompose the system into several sub-systems, then we approximate the arrival rates at each sub-system. Computational results show that the method estimates the system throughput with high accuracy.