cssi/SciSciGPT-SciSciNet huggingface dataset:
Ecological Succession of Bacterial Communities during Conventionalization of Germ-Free Mice

Little is known about the dynamics of early ecological succession during experimental conventionalization of the gastrointestinal (GI) tract; thus, we measured changes in bacterial communities over time, at two different mucosal sites (cecum and jejunum), with germfree C57BL/6 mice as the recipients of cecal contents (input community) from a C57BL/6 donor mouse. Bacterial communities were monitored using pyrosequencing of 16S rRNA gene amplicon libraries from the cecum and jejunum and analyzed by a variety of ecological metrics. Bacterial communities, at day 1 postconventionalization, in the cecum and jejunum had lower diversity and were distinct from the input community (dominated by either Escherichia or Bacteroides). However, by days 7 and 21, the recipient communities had become significantly diverse and the cecal communities resembled those of the donor and donor littermates, confirming that transfer of cecal contents results in reassembly of the community in the cecum 7 to 21 days later. However, bacterial communities in the recipient jejunum displayed significant structural heterogeneity compared to each other or the donor inoculum or the donor littermates, suggesting that the bacterial community of the jejunum is more dynamic during the first 21 days of conventionalization. This report demonstrates that (i) mature input communities do not simply reassemble at mucosal sites during conventionalization (they first transform into a "pioneering" community and over time take on the appearance, in membership and structure, of the original input community) and (ii) the specific mucosal environment plays a role in shaping the community.
Degradation of toluene and p‐xylene in anaerobic microcosms: Evidence for sulfate as a terminal electron acceptor

The degradation of aromatic hydrocarbons (benzene, toluene, ethylbenzene, p-xylene, o-xylene, 1,3,5-trimethylbenzene, and naphthalene) under anaerobic conditions was studied in column microcosms developed with aquifer material from the vicinity of a gasoline spill at Seal Beach, California. In one column, which did not receive any electron acceptors other than those naturally present (sulfate and carbon dioxide), more than 60% of the toluene was oxidized to CO2. The other six added substrates were not degraded when the toluene supply was constant. In another column, the addition of toluene was discontinued after 126 d, which coincided with the onset of p-xylene degradation. Addition of sulfate, the only electron acceptor that was detected, stimulated the transformation of toluene in batch experiments.
Networking and the Role of the Academic Systems Librarian: An Evolutionary Perspective

This paper explores the role of the academic systems librarian from an evolutionary perspective, with a primary focus on the effect that networking technologies have had on this role. Stages of evolution of this role are described, using examples from the literature and from surveys taken over the past few years. The author discusses new tasks the systems librarian has added as a result of this fundamental technological change, outlines trends in the field that are occurring in reaction to this change, and proposes some thoughts for the next stage of development of the systems librarian role.
Developing a groundwater monitoring system for Albemarle County, Virginia

In recent years, land development activities in rural parts of Albemarle County, Virginia have increased steadily. These activities have resulted in increased public concern for the condition of local groundwater resources. However, there is currently no representative monitoring system in place to track the availability of the countypsilas groundwater. Albemarle has a unique hydrogeology, characterized by a noncontiguous, fractured-bedrock aquifer and therefore requires a customized strategy to monitor the status of its groundwater supply and communicate the results to the public. In order to create a customized solution, the team analyzed survey results from groundwater experts, completed user testing of the current monitoring tool, continued work on the existing groundwater database, and created an initial framework for a groundwater monitoring system.
Embryonic Transcription and the Control of Developmental Pathways

It appears that the initial steps up to the [sea urchin] blastula stage are independent of the quality of the nuclear substance, even though it is essential that the nuclear substance be of a kind capable of existing in the egg. The necessity for particular chromosomes becomes apparent first with the formation of the primary mesenchyme and from then on shows up in all processes as far as development can be observed. . . . With respect to those characters in which we are able to recognize individual variations, the nuclear substance and not the cyte plasmic cell substance imposes its specific character on the developing trait. . . . Earlier stages, for which according to our results, specific chromosomes are not necessary, demonstrate a purely maternal character. . . . I would like to ascribe to the cytoplasm of the sea urchin egg only the initial and simplest properties responsible for differentiation. . . it provides the most general basic form, the framework within which all specific details are filled in by the nucleus.
``Topcolor''; Invited talk presented at "Strongly Coupled Gauge Theories, 1996", Nagoya, Japan, Nov. 1996

We review a class of dynamical models in which top condensation occurs at the weak scale, giving rise to the large top quark mass and other phenomena. This typically requires a color embedding, $SU(3)_c \rightarrow SU(3)_1\times SU(3)_2$. These models imply many signatures addressable in near term experiments at colliders and in fixed target mode.
Diagnostic accuracy of CT coronary angiography.

There is a rich and rapidly growing literature on the diagnostic utility of coronary CT angiography (CTA) and its performance relative to other modalities such as stress testing and invasive coronary angiography. Earlier studies of 16-slice coronary CTA showed wide variability in sensitivity (30%–95%) and some variability in specificity (86%–98%). With 40- and 64-slice coronary CTA, more of the chest is covered with each spin of the gantry, the breath hold is shorter, and there are fewer uninterpretable segments than with 16-slice coronary CTA. The very high negative predictive value is especially helpful in ruling out coronary artery disease in patients who have low to intermediate pretest likelihood of CAD.
Computing in electrical engineering education at Drexel university

The use of computing in the undergraduate curricula of the enhanced educational experience in engineering (E/sup 4/) project and in the discrete signals and systems engineering and microelectronics programs in the Department of Electrical and Computer Engineering at Drexel University is described. Examples that illustrate how the microcomputer has been integrated into a curriculum are discussed. The examples range from introductory courses to advanced electives. >
QUANTUM RESONANCES AND DECAY OF A CHAOTIC FRACTAL REPELLER OBSERVED USING MICROWAVES

The quantum resonances of classically chaotic $n$-disk geometries were studied experimentally utilizing thin 2D microwave geometries. The experiments yield the frequencies and widths of low-lying resonances, which are compared with semiclassical calculations. The long time or small energy behavior of the wave-vector autocorrelation gives information about the quantum decay rate, which is in good agreement with that obtained from classical scattering theory. The intermediate energy behavior shows nonuniversal oscillations determined by periodic orbits.
Mononuclear Iron(II) Dicarbonyls Derived from NNS Ligands – Structural Models Related to a “Pre-Acyl” Active Site of Mono-Iron (Hmd) Hydrogenase

We report the syntheses and characterization of dicarbonyliron complexes derived from tridentate, ortho-substituted Schiff base pyridine/thioether ligands (RNNS). Metalation reactions of RNNS (R = CH3, OCH3) at low temperature (–78 °C) with [Fe(CO)4(Br)2] afforded the desired complexes [(RNNS)Fe(CO)2Br]Br (2-COBr, 3-COBr). Reactions under similar conditions with more sterically demanding ligands [R = quinoline (Q), ClPh] afforded complex salts of the form [(RNNS)Fe(CO)2Br][Fe(CO)3(Br)3] (4-COFe and 5-COFe, respectively). Alternatively, the metalation of the RNNS ligands (for all R ≠ H) with [Fe(CO)4(Br)2] in Et2O at room temperature reliably affords the complex species of type [(RNNS)Fe(CO)2Br][Fe(CO)3(Br)3] (2-COFe, 3-COFe, 5-COFe). The metalation reactions of RNNS at only moderately low temperatures (–20 to 0 °C) result in the loss of CO to form the corresponding trigonal-bipyramidal iron(II) dibromide species of type [(RNNS)FeBr2] (2-Br, 4-Br, 5-Br; μeff ≈ 5.3 μB, S = 2). The IR spectrum of each dicarbonyl cation exhibits two ν(CO) stretches at ≈ 2070 and 2030 cm–1. Low-temperature 1H NMR spectroscopy measurements of 2-CO to 5-CO in CD3CN (–35 to 5 °C) revealed sharp resonances in the diamagnetic region. Under dark conditions, each dicarbonyl species is relatively stable ( Me ≈ Q > ClPh). An examination of the structural parameters reveals that higher photostabilities correlate with shorter Fe–C(O) bond lengths, which are induced by variation of the ortho substituent of the pyridine ring. DFT calculations along the putative photolysis pathway revealed that the bulky ligand substituent (in 5-CO) destabilizes the monocarbonyl intermediate, and this is a likely explanation for its more rapid rate of CO photodissociation. Relevance to a possible “apo-active site” of mono-iron hydrogenase (pre-acyl formation) is discussed.
A scalable method to measure similarity between two EDA-generated timing graphs

This is a case study of the use of graph similarity to correlate the timing models obtained from two electronic design automation (EDA) static timing analysis tools (Altera's Quartus II software versus Synopsys PrimeTime). Timing models are data modelled from the post-layout netlist and parasitics extraction. The field programmable gate array's (FPGA) timing model is used by customers to optimize their designs. As mask designs are constantly revisioned, new timing models are generated and thus the Quartus II software must constantly be updated with the new models. A verification needs to be carried out at every new iteration of timing models to ensure the regression testing of timing models is stable and reliable. This case study discusses one such verification methodology. A timing graph consists of nodes and edges. Edges have weights attached to them that can denote some characteristic, such as timing arc delays in this case. Out of the many graph similarity algorithms in the field, the most cited are edit distance similarity, neighbourhood matching, spectral matching and belief propagation. Neighbourhood matching, which was used in this study, is a point-to-point matching of a node's similarity score based on its neighbourhood's similarity score. The timing graph from the Quartus II software was generated with an in-house Tcl scripting language applications programming interface. The timing graph from PrimeTime was generated from its timing reports. An algorithm was postulated to calculate graph similarity based on edge weights of the graphs. The algorithm compared both graphs and produced a matrix of graph similarity scores for all paired nodes. The algorithm was tested on five data paths taken from the two EDA tools under evaluation. Our results showed good correlation between intuitive similarity measure and our algorithmic calculation.
Improved ground‐based liquid water path retrievals using a combined infrared and microwave approach

100 g/m 2 . A new ground-based retrieval algorithm was developed that retrieves LWP using infrared (8–13 mm and 3–4 mm) and microwave (23.8 and 31.4 GHz) radiance observations, as microwave radiance is sensitive to a large range of LWP (less than 5 to over 1000 g/m 2 ) and infrared radiance is extremely sensitive to LWP less than approximately 60 g/m 2 . The random error in the retrieved LWP is estimated to be less than 4% when the LWP is less than 50 g/m 2 but, for larger LWPs, it increases to at least 12 g/m 2 . The algorithm is also able to retrieve effective radius (re) when the LWP is less than approximately 60 g/m 2 . This new retrieval algorithm was applied to data collected by the Atmospheric Radiation Measurement (ARM) program’s Mobile Facility at Pt. Reyes, California, from July to August 2005. Daytime retrieved re values agree well to airborne in situ observations, with a mean bias of 0.11 mm. A radiative transfer model utilizing the retrieved cloud properties was used to compute the surface and top of the atmosphere fluxes. The flux residuals (observed minus calculated) demonstrate a significant reduction in scatter (approximately a factor of 2 for LWP < 40 g/m 2 ) relative to flux calculations where the cloud properties were determined by the microwave-only retrieval algorithm MWRRET.
Optimal tracking over an additive white Gaussian noise channel

This paper studies the optimal reference tracking problems of finite-dimensional, linear, time-invariant (LTI) systems with an additive white Gaussian noise (AWGN) channel between the controller and the plant. We consider two types of the reference signal: a random variable and a Brownian motion. The power of the tracking error is adopted as the measure of the performance and is to be minimized over all stabilizing two-parameter controllers. We assume the power of the channel input is limited and seek to solve the constrained optimization problem explicitly. It is shown that, besides the power constraint, the lowest power of the tracking error hinges closely on non-minimum phase zeros, the unstable poles and the plant gain.
Plant responses to bacterial N-acyl L-homoserine lactones are dependent on enzymatic degradation to L-homoserine.

Many bacteria use quorum sensing (QS) to regulate phenotypes that ultimately benefit the bacterial population at high cell densities. These QS-dependent phenotypes are diverse and can have signific...
Research on Status of Manifold Generation Modes in Guangdong

In accordance that there are short of resources and increasingly serious contradiction between power supply and power demand in Guangdong province,the paper analyzes generation modes of current thermal power,hydroelectric power,nuclear electric power,wind power and other new energy in combination with status of energy structure,application advantages and disadvantages,opportunity and threat model;it explores interior advantages,disadvantages as well as exterior opportunities and threats of each generation modes and presents strategy for sustainable development of power structure in Guangdong province.
HPLC determination and pharmacokinetics of thiabendazole and its major metabolite 5-OH thiabendazole in equine plasma.

Separate high performance liquid chromatographic methods were developed for thiabendazole ( tbz ) and 5-hydroxy thiabendazole (5-OH- tbz ) determination in horse plasma using 1-methyl-2-phenyl benzimidazole ( mpbz ) as an internal standard. In both methods tbz and 5-OH- tbz were extracted from plasma using organic solvents, injected on to a C-18 column, and eluents monitored by a fluorescence detector. However, mobile phase composition, extraction solvent as well as detector wavelength differed in the two methods. The linear range for tbz was 0·02 to 0·77 μg ml −1 while that for 5-OH- tbz was 0·96 to 8·0 μg ml−1. A commercially available tbz oral suspension was administered to four thoroughbred horses in the following manner: days 1 and 2, 44 mg kg−1; days 4 and 5, 440 mg kg−1. Blood samples were collected during the 24 hours after administration and then analysed for tbz and 5-OH- tbz . Halflives (t½), maximum plasma concentrations (Cmax), area under plasma concentration time curves ( auc O-α), and relative apparent bioavailability (F), were determined using pharmacokinetic equations. The pharmacokinetic parameters varied in the following manner: 1·16 to 13·63 hours (t½), 12 to 131 μg ml−1 × hours ( auc O-α), 3·33 to 8·90 μg ml−1 (Cmax), 1·38 to 0·12 (F) after 44 mg kg−1 and 440 mg kg−1 doses, respectively. The ratios of concentrations of tbz to 5-OH- tbz after oral administration of tbz , were significantly lower for 44 mg kg−1 than 440 mg kg−1 doses. Saturation and, or, product inhibition might be the possible reasons for altered halflives and metabolism of tbz after 440 mg kg−1 doses.
Long Term Follow-Up Studies of Patients Surviving Fulminant Viral Hepatitis

Long term follow-up studies (3 to 46 months) were conducted in 22 patients who had survived severe acute viral hepatitis with coma. Complete clinical and biochemical resolution of the hepatitis was observed in all patients within 45 to 75 days after the onset of the acute hepatitis. The only identifiable sequela of the fulminant episode was the persistence of hepatitis B antigen in 1 of 16 initially hepatitis B antigen-positive patients. Three patients suffered a second attack of acute viral hepatitis 4 to 10 months after recovery from the fulminant episode. Mild unresolved hepatitis followed the second episode in 1 patient. Follow-up liver biopsy made in 13 patients (2 to 37 months after the fulminant episode) showed no liver disease related to the fulminant hepatitis except for mild unresolved hepatitis in the hepatitis B antigen carrier. It appears that patients surviving fulminant viral hepatitis rarely, if ever, develop chronic liver disease, in spite of the extreme degrees of hepatic necrosis occurring during the acute illness.
Oligodendrocyte progenitors isolated directly from developing telencephalon at a specific phenotypic stage: Myelinogenic potential in a defined environment

Oligodendroglia differentiate asynchronously in the developing central nervous system, passing through a series of stages identified by the sequential expression of specific differentiation antigens, culminating in the formation of the myelin sheath. In the work presented here, oligodendrocyte progenitors at a temporally narrow and well-defined phenotypic stage of development have been isolated in high purity and yield directly from postnatal rat telencephalon. This stage is identified by the expression of the O4 antigen, the earliest recognized surface marker specific for the oligodendroglial lineage, but the absence of the differentiation marker galactosylcerebroside (GalC). These O4+ GalC- progenitors first appear at birth (10(5)/telencephalon), 2-3 days before O4+ GalC+ oligodendrocytes. The work presented here demonstrates that a major subpopulation of O4+ GalC- progenitors (80%), which we have termed 'proligodendrocytes', is fully committed to terminal oligodendrocyte differentiation. A relatively small, maximal set of nutritional supplements are sufficient for proligodendrocytes to carry out the myelinogenic cascade of differentiated gene expression in a temporally normal manner, in quantitatively significant amounts, in normal ratios of myelin protein isoforms, and in a regulated relationship to the inclusion of myelin-specific products into myelin-like membrane sheets. An important corollary is that this step of myelinogenesis does not require contact with other cell types, in particular neurones and astrocytes, nor does it require unknown growth factors unique to these cell types. Additionally under these conditions, there exists a developmentally quiescent subpopulation (20%) of O4+ GalC- cells that may have significance for understanding the progenitors previously described in adult brain and suggested to be instrumental in remyelination under pathological conditions.
A Simple In Vivo Method for Assessing Changes of Membrane-Bound Ion Channel Density in Xenopus Oocytes

Heterologous expression systems, such as Xenopus oocytes, are widely used to study the regulation and the structure function relationship of ion channels and transporters. In the case of ion channels, activity can be easily measured by conventional two-electrode voltage clamping. However, this method only measures the sum of the activity of all plasma membrane-bound channels. Therefore, this measurement cannot discriminate between effects on channel density and individual channel activity. To address this shortcoming, we have developed a simple assay to detect changes of membrane-bound channel density in intact oocytes. This nonradioactive assay relies on specific antibody binding in whole live cells utilizing a simple spectrophotometric measurement. This assay is linear over a wide range of channel expression levels and provides a simple cost-effective way of monitoring changes of membrane-bound channel density. Moreover, when the heterologous proteins poorly express at the plasma membrane, this method becomes advantageous to complex biochemical cell fractionation.
Geographic and Contextual Effects on Energy Balance-Related Behaviors and Cancer

This chapter concerns the analysis of geographic and contextual effects on health behaviors related to energy balance, such as diet, weight, and physical activity. We adopt a broad definition of the environment to include not just ambient exposures to toxins, meteorological conditions, or other traditional foci of environmental sciences but also the built, economic, social, and policy aspects of the environment. The chapter includes a selective review of research in this area concerning urban sprawl and obesity, built environment and physical activity, social context and energy balance, and the food environment. We then focus on ongoing challenges to advances in the analysis of contextual effects, including discussion of confounding self-selection as a barrier to causal inference, variable selection and spatial scan statistics, and the general problem of incorporating maps into research on health behavior variables. Experimental and longitudinal designs have not been applied extensively in this field and are required to examine causal associations and to quantify which types of interventions are likely to have the largest effect in specific situations.
Elucidation of factors associated with the maturity-related decline in degradability of big bluestem cell wall.

Big bluestem ( Andropogon gerardii) forage samples were collected from three ungrazed, annually burned pastures at 38, 58, and 97 d after burning. Cell wall material received five treatments: chlorite delignification, chlorite delignification plus alkali extraction, NaOH, NaOCH3 in methanol, or NaBH4. Untreated and treated cell walls were ana- lyzed for carbohydrate composition (glucose, xylose, arabinose, galactose, and uronic acids), acetyl bro- mide lignin, acid detergent lignin, alkali-labile phenol- ics ( p-coumaric and ferulic acids), acetyl groups, and 24- and 72-h in vitro degradabilities of neutral monosaccharides. A number of compositional features, notably concentrations of xylose, core lignin as meas- ured by acetyl bromide lignin, alkali-labile phenolics, and acetyl groups, were well related to the decline in cell wall degradability that occurred with increasing maturity of big bluestem. p-Coumaric acid increased with increasing maturity to a greater extent than did ferulic acid. Acid detergent lignin was not well related to degradability of the cell wall for either the untreated or chemically treated cell walls. Chemical treatments failed to identify any particular cell wall component as being most inhibitory. However, all treatments improved in vitro degradability of the carbohydrate fraction, indicating that components contributing to the undegradability of big bluestem cell wall are sensitive to chemical alteration. Treat- ments involving alkali were most effective for improv- ing degradability of big bluestem cell walls.
SU-G-JeP1-10: Feasibility of CyberKnife Tracking Using the Previously-Implanted Permanent Brachytherapy Seed Cloud

Purpose: Robotic radiosurgery is a salvage treatment option for patients with recurrent prostate cancer. We explored the feasibility of tracking the bolus of permanent prostate implants (PPI) using image recognition software optimized to track spinal anatomy. Methods: Forty-five inert iodine seeds were implanted into a gelatin-based prostate phantom. Four superficial gold seeds were inserted to provide ground-truth alignment. A CT scan of the phantom (120 kVp, 1 mm slice thickness) was acquired and a single-energy iterative metal artifact reduction (MAR) algorithm was used to enhance the quality of the DRR used for tracking. CyberKnife treatment plans were generated from the MAR CT and regular CT (no-MAR) using spine tracking. The spine-tracking grid was centered on the bolus of seeds and resized to encompass the full seed cloud. A third plan was created from the regular CT scan, using fiducial tracking based on the 4 superficial gold seeds with identical align-center coordinates. The phantom was initially aligned using the fiducial-tracking plan. Then the MAR and no-MAR spine-tracking plans were loaded without moving the phantom. Differences in couch correction parameters were recorded in the case of perfect alignment and after the application of known rotations and translations (roll/pitch of 2 degrees; translations XYZ of 2 cm). Results: The spine tracking software was able to lock on to the bolus of seeds and provide couch corrections both in the MAR and no-MAR plans. In all cases, differences in the couch correction parameters from fiducial alignment were <0.5 mm in translations and <1 degree in rotations. Conclusion: We were able to successfully track the bolus of seeds with the spine-tracking grid in phantom experiments. For clinical applications, further investigation and developments to adapt the spine-tracking algorithm to optimize for PPI seed cloud tracking is needed to provide reliable tracking in patients. One of the authors (MD) has received research support and speaker honoraria from Accuray.
Using the Business Origami Technique to Understand Complex Ecosystems

Tracking subtle changes in behavior over time, such as people’s behavior using the Internet, can be challenging for researchers. In addition, trying to evaluate changes for a complex ecosystem that includes multiple members of a household can be an even bigger challenge. In this chapter, we describe a method known as the Business Origami Technique to map out and track behavioral changes in a complex ecosystem such as a household’s Internet usage. The Business Origami Technique is a highly visual method that uses tokens to represent key parts of the ecosystem to answer who, where, and how questions about the ecosystem. We describe how to adapt this method from its traditional paper-based format to a digital format in order to reduce the time and effort participants need to create the origami and improve the longevity of the origami artifacts for a longitudinal study.
A novel device design to lower the on-resistance in GaN trench MOSFETs

GaN is one of the best suited materials for high-power devices due to its superior material properties such as high breakdown field, wide band gap and high saturation drift velocity. Consequently, GaN power devices have gained increased attention in recent years. Numerous vertical GaN power transistors have been demonstrated in the past few years [1-4]. One of the preferred GaN vertical device designs is the trench MOSFET. In the traditional trench MOSFET structure [2-4], the channel forms via p-GaN inversion at the dielectric/p-GaN interface resulting in a relatively high on-resistance due to the poor electron mobility in the channel. In this work, we present a novel device design to lower the on-resistance in a trench MOSFET. By inserting a MOCVD regrown GaN interlayer prior to the dielectric deposition (MOCVD Al 2 O 3 ) on the trenched structure, lower on-resistance is achieved due to enhancement in the electron mobility of the channel. For an optimal GaN interlayer thickness of 10 nm, a low on-resistance (active area) of 0.97 mΩ.cm2 alongside enhancement mode operation (V th = 3 V) is demonstrated.
Abstract 4886: Repair of challenging FFPE DNA improves library success rate and sequencing quality

Formalin-fixed, paraffin-embedded (FFPE) clinical samples are an invaluable source of information about genetic alterations in human disease, especially cancer. Next generation sequencing is a powerful tool to mine that information. Unfortunately, sequencing DNA from FFPE samples is challenging due to limited quantities and poor quality, a result of DNA damage incurred during fixation and storage. In this study, we investigated the effects of DNA repair on library preparation and sequencing from FFPE samples. We evaluated a repair enzyme mix that is designed to work on a broad range of DNA damage including modified bases, nicks, gaps, and blocked 3′ ends. Results from FFPE DNA samples of varying quality show that DNA repair generally increases library yields by 10-170%, with the largest improvement on samples of poor quality. Careful analysis of sequencing data shows that base calling qualities for all 4 bases are improved upon DNA repair. Aberrant G:C to A:T mutation were significantly reduced, consistent with cytosine deamination being induced during fixation and storage at room temperature. Interestingly, sequencing miscalls for base pair changes not typically associated with fixation were also reduced. We are currently investigating the source of these mutations. With DNA repair a noticeably positive impact on read mapping and read pairing was observed, resulting in the generation of more useable data. Pretreatment of FFPE DNA by the repair enzyme mix is easily implemented upstream of library construction, allowing fast turnaround time and easy automation. We expect that these improvements will enable the analysis of many FFPE samples that would otherwise not be accessible. Citation Format: Pingfang Liu, Lixin Chen, Laurence Ettwiller, Christine Sumner, Fiona Stewart, Eileen Dimalanta, Theodore Davis, Thomas Evans. Repair of challenging FFPE DNA improves library success rate and sequencing quality. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4886. doi:10.1158/1538-7445.AM2015-4886
Current Status of Practical Applications: Probiotics in Dairy Cattle

The gastrointestinal microbial population of dairy cattle is dense and diverse and can be utilized to reduce pathogenic bacterial populations as well as improve animal productivity and environmental effects. Because of the nature of the dairy industry, probiotic products have been widely used to enhance milk production and the feed efficiency. The individual efficacy of probiotics in dairy cattle is due to specific microbial ecological factors within the gut of the food animal and its native microflora that alter the competitive pressures of the gut. This chapter explores the ecology behind the efficacy of probiotic products against food-borne pathogens that inhabit food animals.
Pressure sensitivity and phenotypic changes in patients with suspected opioid-induced hyperalgesia being withdrawn from full mu agonists.

Objectives: To assess changes in phenotype and pressure sensitivity in patients with suspected opioid-induced-hyperalgesia (OIH) after transitioning to buprenorphine. Methods: Twenty patients with suspected OIH were enrolled to transition to buprenorphine therapy. Patients completed validated self-report measures at baseline and at 1, 4, 8 weeks, and 6 months after initiation of buprenorphine along with quantitative sensory testing including measures of pressure pain threshold, pain tolerance and Pain 50 (a pain intensity rating). Results: 20 patients were enrolled, 17 were treated with buprenorphine and 11 completed all assessment points. We found that after transitioning to buprenorphine, patients on higher opioid doses (≥100mg oral morphine equivalents) had significant improvements for some measures including decreased pain severity and fibromyalgia survey scores, fewer neuropathic pain features, less catastrophizing, fewer depressive symptoms, and improved functioning 1-week after transitioning to buprenorphine with an eventual return back to baseline. Although not statistically significant, patients on high dose opioids (≥100mg OME) also showed a trend of decreased pressure sensitivity 1-week after transitioning to buprenorphine with a gradual return back to baseline. Conclusions: Our study is the first to look at pressure pain sensitivity in patients who were taking opioids and transitioned to buprenorphine. These results suggest that the patients most likely to benefit from buprenorphine therapy are those on higher doses. In addition, the eventual return back to baseline on measures of pain phenotype and pressure sensitivity suggests that buprenorphine may over time result in a return of the hyperalgesic effects of a full mu agonist. Journal of Nature and Science (JNSCI), 3(2):e319, 2017
The Evolving Practice of Psychiatry in the Era of Integrated Care

Background Integrating behavioral health care into the primary care setting is increasingly recognized as an effective way to manage mental illness and substance use disorders on a population level in the United States. The term "integrated care," however, is used in many ways and encompasses several different models. Objectives The aim of this article is to provide a conceptual framework to understand the landscape of models of integrated care and to use this framework to contrast the roles of behavioral health providers in integrated settings with those in traditional behavioral health delivery models. We will also review some of the advantages and limitations of integrated care for health care delivery systems, patients, and primary care providers.
Gas Suppression via Copper Interlayers in Magnetron Sputtered Al-Cu2O Multilayers.

The use of thin-foil, self-propagating thermite reactions to bond components successfully depends on the ability to suppress gas generation and avoid pore formation during the exothermic production of brazes. To study the mechanisms of vapor production in diluted thermites, thin film multilayer Al–Cu–Cu2O–Cu foils are produced via magnetron sputtering, where the Cu layer thickness is systematically increased from 0 to 100 nm in 25 nm increments. The excess Cu layers act as diffusion barriers, limiting the transport of oxygen from the oxide to the Al fuel, as determined by slow heating differential scanning calorimetry experiments. Furthermore, by adding excess Cu to the system, the temperature of the self-propagating thermite reactions drops below the boiling point of Cu, eliminating the metal vapor production. It is determined that Cu vapor production can be eliminated by increasing the Cu interlayer thickness above 50 nm. However, the porous nature of the final products suggests that only metal vapor pr...
Effect of Unilateral Nephrectomy and its Accompanying Hemodynamic Changes on Calcium and Phosphate Excretion in the Dog

Acute unilateral nephrectomy (AUN) results in a prompt increase in electrolyte excretion by the controlateral kidney in the dog (1). Humphreys and Ayus have shown that this increased electrolyte excretion by the remaining kidney consists mainly of Na+ and K+ and is accompanied by striking systemic hemodynamic changes (2). The latter consists of a drop in cardiac output; an increase in diastolic pressure and total peripheral resistance; but a constant glomerular filtration rate. These findings resemble those observed following closure of a systemic arteriovenous fistula (3, 4). Of particular interest in this regard is the fact that when an artificial arteriovenous fistula is created at the time of uninephrectomy, all of the changes seen following AUN are abolished only to reappear again when the fistula is closed. Thus, it is evident that AUN induces hemodynamic changes resembling those seen following closure of a systemic arteriovenous fistula and that the observed increase in electrolyte excretion following AUN is not the result of the removal of the kidney itself, but rather secondary to the hemodynamic changes induced by the AUN.
Posttraumatic Reactions to Psychosis: A Qualitative Analysis

The current study aimed to evaluate the potentially traumatic aspects of psychotic symptoms and psychiatric treatment of psychosis using qualitative methods. Participants included 63 people with First Episode Psychosis or multiple psychotic episodes. Quasi-structured interviews were used to explore those aspects of symptoms and treatment that were perceived as traumatic Emotional reactions to the most traumatic aspect of symptoms and treatment, during and after the event, were also examined. Participants described a number of traumatogenic aspects of psychotic symptoms, including frightening hallucinations; suicidal thought/ attempts, thoughts/ attempts to hurt others; paranoia/delusions and bizarre/disorganized behavior or catatonia. Traumatic aspects of psychosis elicited emotions including anger, sadness and confusion, anxiety and numbness at the time of event. Furthermore, many participants found aspects of treatment to be traumatic, including: being forced to stay in the hospital for a long time; experiencing upsetting side-effects; coercive treatments, including involuntary hospitalization, use of restraints, and forced medication; being exposed to aggressive patients; and mistreatment by professionals. These experiences elicited emotions of anger, sadness, distrust, and a sense of helplessness. Study findings suggest that the experiences both of psychotic symptoms and psychiatric treatment are potentially traumatic can be a powerful barrier to engaging people in mental health services and facilitating recovery. Clinical implications were discussed. Keywords: Trauma, Psychosis, PTSD, Treatment
Sensitivity Analysis of Direct Simulation Monte Carlo Parameters for Ionizing Hypersonic Flows

This work investigates the sensitivity of direct simulation Monte Carlo input parameters for a high-temperature hypersonic flow scenario. The Computation of Hypersonic Ionizing Particles in Shocks ...
Getting political about patient advocacy.

I'M A SECOND-CAREER nurse. In 1999, at the age of 40, I graduated with honors from a nursing program in a large New Jersey community college. Last year, I obtained my MSN in nursing leadership and education, and I'm now taking business courses for pleasure. At this rate, I'll still be in
The SSATS Algorithm and Subspace Methods

This chapter summarizes the development of the State Space Aoki Time Series algorithm since its inception in 1983 as an instrumental variables method, and relates it to subspace methods popular in the engineering literature from the viewpoint of orthogonal projections. Except for the numerical method used to calculate orthogonal projections these two classes of methods are conceptually equivalent.2
How influential are you: detecting influential bloggers in a blogging community

Blogging is a popular activity with high impact on marketing, shaping public opinions, and informing the world about major events from a grassroots point of view. Influential bloggers are recognized by businesses as significant forces for product promotion or demotion, and by oppressive political regimes as serious threats to their power. This paper studies the problem of identifying influential bloggers in a blogging community, BlogCatalog, by using network centrality metrics. Our analysis shows that bloggers are connected in a core-periphery network structure, with the highly influential bloggers well connected with each others forming the core, and the non-influential bloggers at the periphery. The six node centrality metrics we analyzed are highly correlated, showing that an aggregate centrality score as a measure of influence will be stable to variations in centrality metrics.
Kinematic Analyses of Ornithopod Jaw Mechanisms

The aim of kinematic analysis of ornithopod jaw systems is to find and explain correlations between feeding function and aspects of the morphology of the apparatus (i.e., shape and relative dimensions of skeletal elements and joints and their spatial relationships). For organisms such as ornithopods without closely related living descendants to act as experimental surrogates, it is not possible to rely with any great certainty on reconstructions of cranial musculature, since it is clear from electromyographic studies (Weijs and Dantuma 1975; Gans et al. 1978; Herring et al. 1979; Hiiemae 1978) that each jaw muscle participates in various feeding activities, but not to the same extent (contra one muscle = one action), therefore making it impossible to deduce muscle-firing sequences (recruitment of muscle action) for any set of masticatory muscles. Kinematic analyses allow modeling of complex jaw systems through manipulation of spatial relationships of the skull without making assumptions about the muscular system.
Young adults report increased pleasure from using e-cigarettes and smoking tobacco cigarettes when drinking alcohol

Abstract Background Cigarettes share a high rate of co-use with alcohol, particularly among young adults. Studies have demonstrated greater perceived pleasure from smoking cigarettes when drinking alcohol. However, little is known about co-use of electronic cigarettes (e-cigs) and alcohol. The current study sought to compare extent of use and perceived pleasure from cigarettes and e-cigs when drinking alcohol. Methods Young adult bar patrons in California cities (San Diego, Los Angeles, and San Francisco) were recruited in 2015–16 using randomized time-location sampling. Participants completed cross-sectional surveys in bars, reporting the percent of cigarette smoking/e-cig use that occurred under the influence of alcohol, and reported if pleasure from smoking cigarettes/using e-cigs changed when drinking alcohol. Analyses are limited to participants reporting current (past 30-day) use of cigarettes, e-cigs, and alcohol (N = 269; M age = 24.1; 40.1% female, 36.1% Non-Hispanic White). Results Participants reported a greater percentage of cigarette smoking compared to e-cig use under the influence of alcohol (cigarettes M = 63.6%; e-cigs M = 46.7%; p Conclusions Drinking alcohol is associated with increases in perceived rewarding effects of both cigarettes and e-cigs and thus may increase their abuse liability. This effect may be stronger for cigarettes, which could be an important barrier to switching completely from smoking cigarettes to using e-cigs, or quitting both entirely.
Changes in Bile Acid Metabolism, Transport, and Signaling as Central Drivers for Metabolic Improvements After Bariatric Surgery.

We review current evidence regarding changes in bile acid (BA) metabolism, transport, and signaling after bariatric surgery and how these might bolster fat mass loss and energy expenditure to promote improvements in type 2 diabetes (T2D) and nonalcoholic fatty liver disease (NAFLD). The two most common bariatric techniques, Roux-en-Y gastric bypass (RYGB) and vertical sleeve gastrectomy (VSG), increase the size and alter the composition of the circulating BA pool that may then impact energy metabolism through altered activities of BA targets in the many tissues perfused by systemic blood. Recent reports in human patients indicate that gene expression of the major BA target, the farnesoid X receptor (FXR), is increased in the liver but decreased in the small intestine after RYGB. In contrast, intestinal expression of the transmembrane G protein-coupled BA receptor (TGR5) is upregulated after surgery. Despite these apparent conflicting changes in receptor transcription, changes in BAs after both RYGB and VSG are associated with elevated postprandial systemic levels of fibroblast growth factor 19 (from FXR activation) and glucagon-like peptide 1 (from TGR5 activation). These signaling activities are presumed to support fat mass loss and related metabolic benefits of bariatric surgery, and this supposition is in agreement with findings from rodent models of RYGB and VSG. However, inter-species differences in BA physiology limit direct translation and mechanistic understanding of how changes in individual BA species contribute to post-operative improvements of T2D and NAFLD in humans. Thus, details of all these changes and their influences on BAs’ biological actions are still under scrutiny. Changes in BA physiology and receptor activities after RYGB and VSG likely support weight loss and promote sustained metabolic improvements.
A novel geriatric assessment tool that predicts postoperative complications in older adults with cancer.

Abstract Introduction Comprehensive geriatric assessment prior to oncologic surgery can help predict surgical outcomes. We tested whether an abbreviated geriatric assessment tool, the Vulnerable Elderly Surgical Pathways and outcomes Assessment (VESPA), would predict post-operative complications among older adults undergoing oncologic surgery. Method From 2008 to 2011, geriatric assessments were completed using the VESPA tool for patients age ≥ 70 seen in a pre-operative clinic. The VESPA assessed functional status, mood, cognition, and mobility, and can be completed in Results A total of 476 patients who underwent oncologic surgery received the assessment using VESPA. Compared to patients with low VESPA scores ( Conclusion The VESPA identifies older patients with cancer who are at risk for postoperative surgical and geriatric complications as well as functional needs at hospital discharge.
A method for assessing histone surface accessibility genome-wide

The assembly of DNA into nucleosomes and higher order chromatin structures serves not only as a means of compaction but also organizes the genome to facilitate crucial processes such as cell division and regulation of gene expression. Chromatin structure generally limits access to DNA, with the accessibility of DNA in chromatin being regulated through post translational modification of the histone proteins as well as the activity of chromatin remodeling proteins and architectural chromatin factors. There is great interest in assessing chromatin accessibility genome-wide to identify functional elements associated with enhancers, promoters, and other discontinuities in the compacted chromatin structure associated with gene expression. As the vast majority of techniques rely upon assessment of the exposure of the underlying DNA, we describe here a general method that can be used to assess exposure of internal and external histone protein surfaces. We demonstrate the feasibility of this method, in the organism S. cerevisiae. Our method relies on substitution of residues residing on selected histone protein surfaces with cysteine, and assessment of exposure by reaction with a thiol specific reagent, biotin-maleimide. We demonstrate that modified nucleosomes can be efficiently excised from nuclei treated with the reagent via a one-step purification process. After library preparation and deep sequencing, selected nucleosomes are typically ~25-fold enriched over background signals and exhibit phasing with respect to transcription start sites in yeast that is identical to an unselected population.
Joint Mathematics Meetings 2020

1.Infuriating gaming delays5.____ order: public commentary ban8.Closest pal, in text-speak11.“Thanks ____!”12.Actress McDonald with six Tony Awards14.Old West lawman Wyatt16.Chimney channel17.* Raj...