cssi/SciSciGPT-SciSciNet huggingface dataset:
The evolutionary and biogeographic history of the armoured harvestmen – Laniatores phylogeny based on ten molecular markers, with the description of two new families of Opiliones (Arachnida)

We investigated the internal phylogeny of Laniatores, the most diverse suborder of Opiliones, using sequence data from 10 molecular loci: 12S rRNA, 16S rRNA, 18S rRNA, 28S rRNA, cytochrome c oxidase subunit I (COI), cytochrome b, elongation factor-1α, histones H3 and H4, and U2 snRNA. Exemplars of all previously described families of Laniatores were included, in addition to two families – Petrobunidae, fam. nov. and Tithaeidae, fam. nov. – that we erect herein. Data analyses were based on maximum likelihood and Bayesian approaches on static alignments, and included phylogenetic tree estimation, molecular dating, and biogeographic analysis of ancestral area reconstruction. The results obtained include the monophyly of Laniatores and the infraorder Grassatores – the focus of this study – as well as support for numerous interfamilial relationships. The two new families described cluster with other South-east Asian families (Podoctidae and Epedanidae). Diversification of Laniatores is estimated at ~348 Mya, and origin of most Grassatores superfamilies occurs in a ~25 million year span of time immediately after the end-Permian mass extinction (254 Mya). Ancestral range reconstruction of the clade (Samooidea + Zalmoxoidea) suggests that the ancestral range of Samooidea comprises West Tropical Gondwana (West Africa + Neotropics), whereas that of Zalmoxoidea is exclusively Neotropical. The following additional taxonomic changes are proposed: (1) Remyus is transferred to Phalangodidae, and (2) Escadabiidae and Kimulidae are transferred to Zalmoxoidea.
Shock interactions in the outer heliosphere

The results of recent simulations of the nonlinear evolution of the solar wind structures are reviewed, emphasizing theoretical development and the shock interactions model (SIM). Models which calculate jumps in flow properties across shocks without using exact Rankine-Hugoniot relations and models which do use them are addressed. The development of a computer code and some basic applications to the SIM are considered. Simulation results for the formation and propagation of forward-reverse shock pairs and the collision and merging of shocks are shown. Two studies which used the SIM to simulate nonlinear evolution of large-scale solar wind structures in the outer heliosphere are examined, and the SIM is then applied to study the heating of the solar wind in the outer heliosphere. The results support the hypothesis that shocks are mainly responsible for the heating of the solar wind plasma in the outer heliosphere at least up to 30 AU.
Origins of activity patterns in self-organizing neuronal networks in vitro

Nerve cell ensembles growing in culture on microelectrode arrays allow long-term, multisite monitoring of spontaneous and evoked action potential (spike) activity. These ensembles generate complex spatio-temporal spike patterns and constitute evolving non-linear and non-stationary dynamical systems. They provide effective platforms for observations of the internal dynamics of neuronal networks, especially pattern generation and the evolution of network organization. Nerves cells in cultures form many small neuronal clusters (termed nacelles) in which substantial membrane contact is achieved. We propose that such morphological clusters generate subthreshold interactions that can lead to noise-induced membrane potential oscillations with frequent ignition to spiking. Recruitment of several nacelles and dispersed neurons then leads to dynamically organized circuits capable of reliably generating and maintaining a specific burst pattern. The observed coexistence of different burst patterns suggests network substructures (circuits) with autonomous activity. Entrainment of all circuits to a global pattern is thought to represent a network decision state with automatic fault-tolerant output. Such phenomena suggest that not only the redundancy of connections but also the form of the message are important factors in the creation of fault-tolerance.
Guest Editors' Note: Special Issue on Large-Scale Parallel Processing

We are now nearly a decade into the regime of having to depend on scaling of parallelism, rather than clock rate, for increases in performance. Core densities on chips have been steadily increasing, along with the overall number of processor chips in large scale systems. Early in this phase, it was possible to extend existing techniques to cope with the issues of scaling. But now we are consistently encountering new problems requiring novel solutions. The papers in this issue are representative of the range of problems that must be addressed, from power, to memory architecture, to software infrastructure, and handling performance faults in production runs, we see how fundamental changes in approach are now emerging to support continued scaling.
Cross-species fostering affects meat preferences of wild house mice.

Abstract Wild-strain male house mice were fostered at birth onto conspecifics, deer mice, or domestic Norway rats. In adulthood, their flesh-eating preferences were tested by allowing them to feed from freshly asphyxiated conspecifics and either deer mice or rats. The mice ate significantly more conspecific flesh than contraspecific flesh, except when the flesh offered was that of the contraspecies upon which the mouse had been fostered at birth. The failure of cross-species-fostered mice to discriminate between their own species and their foster species in flesh-preference tests is attributed to their having learned early in life to respond to the foster species in the same way they normally respond to conspecifics, that is, by approaching them, investigating them, and, when finding them dead, feeding upon them.
Variability of particulate matter and abundant zooplankton off the southeastern United States during spring of 1984 and 1985

Abstract The variability of particulate matter, chlorophyll a and zooplankton often depend strongly on physical processes. In this paper we compare distributions observed on the southeastern shelf of the United States during April 1984 and 1985. April 1984 was characterized by high freshwater runoff, vertical stratification and strong wind stress. In April 1985 all three variables were much lower. While alongshore flow was similar in both years, cross-shelf flow was more pronounced in 1984. The most noticeable effect on zooplankton was their expatriation towards offshore. The near surface, offshore and deeper Ekman flows from northeastward wind events, in conjunction with intermittent sinking, tend to trap most particulate matter that was produced nearshore in the nearshore or middle shelf region. Offshore removal was transient following upwelling wind events during stratification conditions. Zooplankton abundance on the inner and middle shelf was not only a function of near- and offshore production but also of cross-shelf and alongshore displacement. Whereas the circumglobal copepod genus Paracalanus occurs abundantly in summer, spring and autumn on the inner and middle shelf, the cosmopolitan genus Oithona which is abundant during summer is scarce during spring and appears to be affected by temperature and water column stability. The variability of particulate matter and zooplankton during early spring seems to be at least partly determined by atmosphere forcing and the amount of freshwater runoff.
Radiographic imaging for treatment and follow-up of developmental dysplasia of the hip

Developmental dysplasia of the hip (DDH) is a spectrum of abnormalities that can range from a very mild disturbance to a very severe process that is incapacitating later in life. This article considers the causative factors and natural history of DDH, as well as anatomic abnormalities, physical examination findings, and both surgical and nonsurgical treatment options. The goal of this article is to place in perspective the use of advanced imaging techniques in the diagnosis and follow-up of patients with DDH. Ultrasound, computed tomography (CT), and magnetic resonance (MR) findings are reviewed with respect to the diagnosis of DDH, treatment complications, and long-term problems that may occur in treated and untreated patients.
Prognostic and biologic significance of DNMT3B expression in older patients with cytogenetically normal primary acute myeloid leukemia

DNMT3B encodes a DNA methyltransferase implicated in aberrant epigenetic changes contributing to leukemogenesis. We tested whether DNMT3B expression, measured by NanoString nCounter assay, associates with outcome, gene and microRNA expression and DNA methylation profiles in 210 older (⩾60 years) adults with primary, cytogenetically normal acute myeloid leukemia (CN-AML). Patients were dichotomized into high versus low expressers using median cut. Outcomes were assessed in the context of known CN-AML prognosticators. Gene and microRNA expression, and DNA methylation profiles were analyzed using microarrays and MethylCap-sequencing, respectively. High DNMT3B expressers had fewer complete remissions (CR; P=0.002) and shorter disease-free (DFS; P=0.02) and overall (OS; P<0.001) survival. In multivariable analyses, high DNMT3B expression remained an independent predictor of lower CR rates (P=0.04) and shorter DFS (P=0.04) and OS (P=0.001). High DNMT3B expression associated with a gene expression profile comprising 363 genes involved in differentiation, proliferation and survival pathways, but with only four differentially expressed microRNAs (miR-133b, miR-148a, miR-122, miR-409-3p) and no differential DNA methylation regions. We conclude that high DNMT3B expression independently associates with adverse outcome in older CN-AML patients. Gene expression analyses suggest that DNMT3B is involved in the modulation of several genes, although the regulatory mechanisms remain to be investigated to devise therapeutic approaches specific for these patients.
Some pharmacological characteristics of the venom of the alphabet cone, Conus spurius atlanticus.

Lyophilized venom of the alphabet cone, Conus spurius atlanticus, was tested on the crabs Uca sp. and Cardisoma guanhumi. The venom induced ataxia, muscle spasms, paralysis, and death in Uca pugilator (ld50 ca. 100 μg per crab). The venom may have interfered with conduction between the cardiac ganglion and the contractile elements of the heart in C. guanhumi.
Ammonia loss from surface applied urea-acid products

Ammonia (NH3) losses from soils occur only under alkaline conditions; therefore, adequate acidification could prevent NH3 loss. In acid soils this alkaline condition will exist only as a micro-environment around the decomposing CO(NH2)2 granule. The objective of this experiment was to examine the degree of NH3 loss reduction that occurs when acids are placed with surface applied CO(NH2)2. Phosphoric acid, H2SO4, HCl and HNO3 were used with surface applied CO(NH2)2 in a laboratory experiment to examine resultant NH3 loss under very extreme NH3 loss conditions. Calcium and magnesium chloride salts were added to urea:phosphoric acid to compare the relative effectiveness of acid and Ca + Mg salts for control of NH3 loss. Little depression of NH3-N loss was found from CO(NH2)2 containing H3PO4 and H2SO4 when the sand contained free CaCO3. However, when CO(NH2)2:H3PO4 (UP) mixtures were applied as 17-19-0 on neutral and acid sands, NH3 losses were reduced. Molar ratios less than 1:1 (28-12-0, 35-7-0) resulted in NH3 losses similar to those from CO(NH2)2 alone even in acid soils. The 110 g N m−2 as 17-19-0 reduced relative NH3-N loss and pH in acidified and neutral soils more effectively than 11 g N m−2. Ammonia losses are determined by chemical reactions occurring under the individual CO(NH2)2 granules; therefore, the use of the high 110 g N m−2 rates in this research. The 17-19-0 reduced soil pH and retarded the rate of CO(NH2)2 hydrolysis with consequent reduction in NH3 loss. Ammonia loss was reduced only slightly at 11 g N m−2 from 17-19-0 even in acid soils. Ammonia loss was reduced from 70 to 30% of applied N by applications of HNO3 and HCl with the CO(NH2)2. The HNO3 and HCl react with CaCO3 in a calcareous soil to produce CaCl2 and Ca(NO3)2 which are known to reduce NH3 loss from surface applied CO(NH2)2. However, a dry product of HNO3 · CO(NH2)2 is explosive and can not be used as a general fertilizer. Calcium chloride or MgCl2 combined with CO(NH2)2:H3PO4 reduced NH3 loss more at 110 g N m−2 than at 11 g N m−2. Calcium chloride reduced NH3 loss more effectively than MgCl2. The CaCl2 and MgCl2 salts were more effective than H2SO4 or H3PO4 in reducing NH3 losses except when (e.g., 17-19-0) mixtures were added to neutral or acidic sands.
Comparison of the Effects of Shiga-like Toxin 1 on Cytokine- and Butyrate-Treated Human Umbilical and Saphenous Vein Endothelial Cells

To examine the reported heterogeneity of endothelial cells to Shiga-like toxin 1 (Stx1), the responses of human umbilical (HUVEC) and saphenous (HSVEC) vein endothelial cells to cytokines, butyrate, and toxin were compared. Untreated HSVEC were generally more susceptible than were HUVEC to Stx1; pretreatment of either cell with lipopolysaccharide, interleukin-1 beta, or tumor necrosis factor-alpha enhanced Stx1 toxicity. Dexamethasone alone increased total globotriaosylceramide (Gb3) content and toxin binding but inhibited cytokine-enhanced cytotoxicity, whereas the differentiation agent, sodium butyrate, increased both Gb3 content and cytotoxicity responses to Stx1, most prominently in HSVEC. Stx1 toxicity directly correlated with the release of von Willebrand factor from HSVEC but not from HUVEC. Thus, HUVEC and HSVEC exhibit distinctive responses to Stx1, cytokines, and butyrate. This suggests the need for caution in extrapolating from in vitro studies utilizing one endothelial cell type to in vivo events during pathogenesis of Stx-mediated thrombotic microangiopathies.
Turnover of the fatty acyl and glycerol moieties of microsomal membrane lipids from liver, gill and muscle tissue of thermally acclimated rainbow trout,Salmo gairdneri

Rainbow trout (Salmo gairdneri) acclimated to 5°C or 20°C were administered 2-3H-glycerol and 1-14C-acetate (63 μCi of each isotope/100 g body weight) via intraperitoneal injection, and subsequently maintained at their respective acclimation temperatures. Total lipid extracts (>80% phospholipid) were prepared from isolated microsomes of liver, gill and muscle tissue at various times over a three week period. Half-lives were determined independently for the fatty acyl and glycerol moieties from slopes of regression lines relating dpm/nmole phospholipidPi vs time. In liver tissue, rates of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) turnover were also determined. Membrane turnover was most rapid in liver followed by gill and muscle. In liver, membrane fatty acids turned over more rapidly in warm-(t1/2=3.4 days) than in cold-(t1/2=6.8 days) acclimated fish, whereas in gill, rates of fatty acid turnover, did not differ significantly between acclimation groups. In contrast, rates of glycerol turnover were independent of acclimation temperature in liver, but faster (t1/2=6.7 days) in warm- than cold- (t1/2=15.1 days) acclimated fish in gill. In total lipid extracts, rates of fatty acid and glycerol turnover were equivalent in warm-acclimated fish, however, in cold-acclimated trout, there was a tendency for fatty acids (t1/2=9.1 days) to turnover more rapidly than glycerol (t1/2=15.1 days) in gill tissue, but more slowly (t1/2=6.82 days) than glycerol (t1/2=4.1 days) in liver. Although rates of glycerol turnover were equivalent in PC and PE of liver microsomes, the fatty acyl component turned over significantly more rapidly in PC at both acclimation temperatures. In cold-acclimated trout, rates of fatty acid and glycerol turnover were equivalent in PE, but the fatty acyl moiety of PC (t1/2=4.7 days) turned over significantly more rapidly than glycerol (t1/2=7.5 days). These results were interpreted as indicating that: (1) acclimation temperature independently influenced rates of fatty acid and glycerol turnover in a tissue specific manner, (2) a deacylation-reacylation pathway was activated in both liver and gill as a consequence of cold acclimation, but that liver tissue was more effective than gill in reutilizing the fatty acids released by phospholipase activity, and (3), in liver microsomes, patterns of turnover were phospholipid specific, with PC and PE differing either in the susceptibility of their acyl groups to degradation, or in their ability to reutilize fatty acids cleaved during membrane turnover at cold temperatures.
Impacts of Farm Structural Change on Farmers' Social Ties

ABSTRACT Many studies have examined how changes in extractive and basic industries affect natural-resource-dependent rural communities. Most of these studies have used aggregate data to explore the impacts of natural resource dependency and change on indicators of economic well-being. However, there are many reasons to believe that changes in the size and structure of natural resource industries also affect the dynamics of social life in these communities. Persons who play diverse roles in local natural resource sectors are likely to experience different impacts from economic restructuring. In this article we analyze data from nine dairy-farm-dependent rural communities in seven states to explore the impacts of agricultural restructuring on levels of farm operator community involvement and social integration. Comparisons are made at the aggregate level across communities dominated by different types of dairy operations, and at the individual level across dairy farmers who run different-sized operations.
Differential activation of human core, non-core and auditory-related cortex during speech categorization tasks as revealed by intracranial recordings

Speech perception requires that sounds be transformed into speech-related objects with lexical and semantic meaning. It is unclear at what level in the auditory pathways this transformation emerges. Primary auditory cortex has been implicated in both representation of acoustic sound attributes and sound objects. While non-primary auditory cortex located on the posterolateral superior temporal gyrus (PLST) is clearly involved in acoustic-to-phonetic prelexical representations, it is unclear what role this region plays in auditory object formation. Additional data support the importance of prefrontal cortex in the formation of auditory objects, while other data would implicate this region in auditory object selection. To help clarify the respective roles of auditory and auditory-related cortex in the formation and selection of auditory objects, we examined high gamma activity simultaneously recorded directly from Heschl’s gyrus (HG), PLST and prefrontal cortex, while subjects performed auditory semantic detection tasks. Subjects were patients undergoing evaluation for treatment of medically intractable epilepsy. We found that activity in posteromedial HG and early activity on PLST was robust to sound stimuli regardless of their context, and minimally modulated by tasks. Later activity on PLST could be strongly modulated by semantic context, but not by behavioral performance. Activity within prefrontal cortex also was related to semantic context, and did co-vary with behavior. We propose that activity in posteromedial HG and early activity on PLST primarily reflect the representation of spectrotemporal sound attributes. Later activity on PLST represents a prelexical processing stage and is an intermediate step in the formation of word objects. Activity in prefrontal cortex appears directly involved in word object selection. The roles of other auditory and auditory-related cortical areas in the formation of word objects remain to be explored.
Residual demand estimation for market delineation: Complications and limitations

To shed some light on market delineation in an antitrust context, many economists are turning to estimates of residual demand elasticities. Recent papers have drawn attention to the importance of demand curve in market delineation and explained how they can be estimated. This paper shows that there are many complications and limitations of the approach. The relationship between the residual demand elasticity and the scope of the relevant market is complicated and depends on behavioral assumptions. The residual demand elasticity that can be estimated is not the one on which market delineation turns. The estimation of residual demand elasticities can be very difficult because of the complex dynamics of consumer behavior. Finally, residual demand estimators are likely to have a high variance because of instrument problems and this is likely to lead to widely varying estimates depending on specification choices.
Utilizing Formative Assessments to Guide Student Learning in an Interactive Physics Learning Environment.

In the last decades, many education researchers have been trying to use computerized learning environments to enhance student learning. Without proper instructional supports and guidance, however, students often failed to acquire knowledge from computer-based learning activities. The objective of this study was to demonstrate how research-based formative assessment questions could be used as a framework for providing appropriate scaffolding in a computerized physics learning environment. To achieve this goal, an interactive physics tutor named APT (Assessment-based interactive Physics Tutor) was developed using Java and Open Source Physics. Examples of learning activities in APT were presented in order to highlight how formative assessment questions could be utilized to provide various instructional supports and guidance (e.g., prompting questions, descriptive statements, and computer simulations) tailored to the student's misconceptions. Educational implications of using APT were also discussed.
Development of a Multilevel Framework to Increase Use of Targeted Evidence-Based Practices in Addiction Treatment Clinics.

Implementing specific evidence-based practices (EBPs) across a set of addiction treatment providers have been a persistent challenge. In the Advancing Recovery(AR) demonstration project, single state agencies, the entities that distribute federal funds for substance use disorder prevention and treatment services, worked in partnership with providers to increase the use of EBPs in the treatment of addiction. The project supported two cohorts of six 2-year awards. Field observations from the first year of implementation guided development of a multilevel framework (the Advancing Recovery Framework). Government entities and other payers can use the framework as a guide for implementing evidence-based clinical practices within treatment networks. The Advancing Recover Framework calls for a combination of policy and organizational changes at both the payer (government agency) and provider levels. Using the Advancing Recovery Framework, 11 of the 12 AR payer/provider partnerships increased use of clinical EPBs. This article identifies key payer policy changes applied during different phases of EBP program implementation. The public health benefit of the demonstration project was broader use of medication–assisted therapy and continuing care in addiction treatment services.
Optimal discovery of a stochastic genetic network

In this paper, we present a parameter identification algorithm for the discovery of a genetic regulatory network. The genetic network is modeled, via a mechanistic approach, as a nonlinear stochastic regulatory network, in which transcription, translation and degradation processes are described as discrete stochastic events which depend nonlinearly on the number of molecules inside the cell. The system depends on several unknowns, namely the rates of transcription, the rates of translation and the degradation rates. Furthermore, the system is observable through the measure, at regular time intervals, of the factorial cumulants of the molecule counts. The unknown parameters are uncovered by studying the system output response to an arbitrary command input. The parameter search is posed as an optimization program, in which the cost function is the deviation between the observed factorial cumulants and the model output, and in which the constraint is the parameterized ordinary differential equation (ODE) governing the time evolution of the factorial cumulants. The optimization problem is solved via an adjoint-based quasi- Newton algorithm. The command input is found to have an important impact on the parameter search: Oscillatory input signals yield better parameter discovery than flat input signals. Finally, numerical results are presented for two systems: a Hill feedback and a Michaelis Menten process.
Video-assisted thoracic surgery (VATS) resection for lung cancer

VATS is a relatively new technology that has become the standard of care for basic procedures such as drainage of pleural effusion and blebectomy. VATS anatomic lung resection is more controversial. Published studies demonstrate several advantages of VATS over a standard posterolateral thoracotomy. A minimally invasive approach causes less inflammatory reaction. Acute and chronic pain are diminished. As a result, the length of hospitalization is shorter. Early and late shoulder dysfunction is less and return to work time is shorter. Taken together, these factors suggest a better overall outcome using a VATS approach. From an oncologic standpoint, lymph node dissection can be accomplished and locoregional recurrence is low. The validity of VATS for lung cancer will be determined by long-term data. A phase III national (intergroup) protocol is being drafted and will help to answer these questions.
Encapsulation of Inorganic Particles with Nanostructured Cellulose

Inorganic-cellulose core-shell and hollow cellulose nanoparticles were prepared by self-encapsulation with regenerated cellulose in a poly(acrylic acid) hydrogel layer surrounding inorganic particle templates in N-methylmorpholine oxide (NMMO) (4-methylmorpholine N-oxide) monohydrate solution. The hydrogel layer surrounding the inorganic particle surface plays a decisive role in the core-shell formation. The core-shell nanostructures were characterized using TEM, SEM, and X-ray diffraction (XRD). The cellulose shell was found to be composed of cellulose spheres or nodules with dimensions of approximately 30 nm. Individual, regenerated cellulose nanoparticles were also synthesized by addition of nonsolvent under agitation to dilute solutions of cellulose dissolved in NMMO. The effects of the rate of addition of water (the nonsolvent) on the nanostructure, morphology and crystallinity of the regenerated cellulose nanoparticles were studied. The results indicate that the faster the water-addition rate, the smaller the cellulose nanoparticles formed.
Viscosity‐Temperature Relation for Network Liquids

The viscosity-temperature relation for the network liquids is considered in the light of the results for associated liquids and polymers. A critical examination of all the data available indicates that for liquid B2O3, SiO2, and BeF2 the energy of activation for flow is temperature dependent. Liquid GeO2 is possibly an anomaly. Empirical equations which satisfactorily describe the viscosity of associated liquids are not applicable to liquid B2O3 and SiO2.
Conflict Resolution and Traffic Complexity of Multiple Intersecting Flows of Aircraft

This paper proposes a general framework to study the conflict resolution for multiple intersecting flows of aircraft in planar airspace. The conflict-resolution problem is decomposed into a sequence of subproblems, each involving only two intersecting flows of aircraft. The strategy for achieving the decomposition is to laterally displace the aircraft flows so that they intersect in pairs, and the resulting conflict zones have no overlap. A conflict zone is defined as a circular area that is centered at the intersection of a pair of flows, which allows aircraft approaching the intersection to resolve the conflict completely within the conflict zone without straying outside. An optimization problem is then formulated to minimize the lateral displacements of the aircraft flows. Although this optimization problem is difficult to solve in general due to its nonconvex nature, a closed-form solution can be obtained for three intersecting flows. The minimum requirement of lateral displacements of aircraft flows for conflict resolution can also be used as a metric of traffic complexity for multiple intersecting flows of aircraft. It is shown that the order of growth of this complexity metric is O(n 3) for symmetric configurations of n flows of aircraft.
Design of oversampled DFT modulated filter banks optimized for acoustic echo cancellation

This paper describes a method for designing oversampled DFT filter banks (FB) optimized for subband acoustic echo cancellation (AEC). For this application, the design requirements typically are good echo cancellation quality, low delay, small reconstruction error, and low computation complexity. Our method explicitly includes a model for echo return loss enhancement (ERLE) as part of the optimization criteria. Convergence of the high-dimensional, nonlinear optimization problem is facilitated by decorrelating the prototype filter impulse response via a discreet cosine transform (DCT), discarding many insignificant coefficients and thus reducing the dimensionality of the search. The experimental results demonstrate the effectiveness of our design and the effects on the performance of AEC, with ELRE improvements on the order of 3 dB or better. The method is flexible and could also be extended to other application domains.
A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011

The initial genome-scale reconstruction of the metabolic network of Escherichia coli K-12 MG1655 was assembled in 2000. It has been updated and periodically released since then based on new and curated genomic and biochemical knowledge. An update has now been built, named iJO1366, which accounts for 1366 genes, 2251 metabolic reactions, and 1136 unique metabolites. iJO1366 was (1) updated in part using a new experimental screen of 1075 gene knockout strains, illuminating cases where alternative pathways and isozymes are yet to be discovered, (2) compared with its predecessor and to experimental data sets to confirm that it continues to make accurate phenotypic predictions of growth on different substrates and for gene knockout strains, and (3) mapped to the genomes of all available sequenced E. coli strains, including pathogens, leading to the identification of hundreds of unannotated genes in these organisms. Like its predecessors, the iJO1366 reconstruction is expected to be widely deployed for studying the systems biology of E. coli and for metabolic engineering applications.
Comparison of multiuser diversity using STBC and transmit beamforming with outdated feedback

For multiuser diversity systems employing adaptive modulation, we compare the spectral efficiency for space-time block coding (STBC) and transmit beamforming (BF) with outdated channel feedback. Taking into account the channel feedback delay, we derive the optimal thresholds to maximize spectral efficiency subject to an average BER constraint, and illustrate the impact of feedback delay on the achievable multiuser diversity gain with either STBC or BF. We observe that more transmit antennas bring higher spectral efficiency for BF But this becomes inverted using STBC, due to the effect of channel-hardening. With a small feedback delay, the BF scheme outperforms the STBC scheme. However, when feedback delay becomes large enough, the STBC scheme achieves higher spectral efficiency due to the reduced diversity order of BF.
GABAergic innervation of the Mauthner cell and other reticulospinal neurons in the goldfish.

The Mauthner cells are pair of identifiable hindbrain neurons that participate in the escape response of fishes. Membrane excitability in these cells is regulated by inhibitory neurons that use glycine as a transmitter. We examined the possibility that the inhibitory transmitter gamma-amino butyric acid (GABA) may also act on the Mauthner cells. We used immunocytochemical methods involving an antibody against glutamic acid decarboxylase (GAD), the synthesizing enzyme for GABA. Our study revealed dense GAD immunoreactive terminals surrounding the Mauthner cells. Puncta counts showed that the distribution of GAD immunoreactivity was densest at the distal lateral dendrite of the Mauthner cells; the distribution of puncta tapers gradually in regions closer to the soma. The axon cap was devoid of GABAergic immunoreactivity. We also performed unilateral lesions of the octaval nuclei to evaluate the origin of the GAD immunoreactive terminals. Following the lesions, we found marked decreases in GAD immunoreactive terminals on the proximal lateral dendrite, soma, and proximal ventral dendrite of both Mauthner cells. These results suggest that the octaval region contributes to bilateral inhibition of the Mauthner cells. The distal lateral dendrite of the ipsilateral Mauthner cell also showed a reduction in GAD immunoreactive terminals. This suggests that GABA mediates remote dendritic inhibition of this cell. GAD immunoreactive puncta also surrounded other large reticulospinal neurons, some of which are serially reiterated along the anterior-posterior axis of the hindbrain. Thus, GABA may also exert an influence not only on the Mauthner cells, but also on other reticulospinal neurons. © 1993 Wiley-Liss, Inc.
Autism and dietary therapy: case report and review of the literature.

We report the history of a child with autism and epilepsy who, after limited response to other interventions following her regression into autism, was placed on a gluten-free, casein-free diet, after which she showed marked improvement in autistic and medical symptoms. Subsequently, following pubertal onset of seizures and after failing to achieve full seizure control pharmacologically she was advanced to a ketogenic diet that was customized to continue the gluten-free, casein-free regimen. On this diet, while still continuing on anticonvulsants, she showed significant improvement in seizure activity. This gluten-free casein-free ketogenic diet used medium-chain triglycerides rather than butter and cream as its primary source of fat. Medium-chain triglycerides are known to be highly ketogenic, and this allowed the use of a lower ratio (1.5:1) leaving more calories available for consumption of vegetables with their associated health benefits. Secondary benefits included resolution of morbid obesity and imp...
Summarization of clinical information: A conceptual model

Background: To provide high-quality and safe care, clinicians must be able to optimally collect, distill, and interpret patient information. Despite advances in text summarization, only limited research exists on clinical summarization, the complex and heterogeneous process of gathering, organizing and presenting patient data in various forms. Objective: To develop a conceptual model for describing and understanding clinical summarization in both computer-independent and computer-supported clinical tasks. Design: Based on extensive literature review and clinical input, we developed a conceptual model of clinical summarization to lay the foundation for future research on clinician workflow and automated summarization using electronic health records (EHRs). Results: Our model identifies five distinct stages of clinical summarization: (1) Aggregation, (2) Organization, (3) Reduction and/or Transformation, (4) Interpretation and (5) Synthesis (AORTIS). The AORTIS model describes the creation of complex, task-specific clinical summaries and provides a framework for clinical workflow analysis and directed research on test results review, clinical documentation and medical decision-making. We describe a hypothetical case study to illustrate the application of this model in the primary care setting. Conclusion: Both practicing physicians and clinical informaticians need a structured method of developing, studying and evaluating clinical summaries in support of a wide range of clinical tasks. Our proposed model of clinical summarization provides a potential pathway to advance knowledge in this area and highlights directions for further research.
Time magnification of electrical signals using chirped optical pulses

The authors report a method for stretching electrical signals in time. A high chirp rate is imposed on the electrical signal by mixing it with a dispersed ultra-short optical pulse in an electro-optic intensity modulator. This is followed by a passive optical dispersion element to produce a time-magnified copy of the input electrical signal.
Caudal brainstem processing is sufficient for behavioral, sympathetic, and parasympathetic responses driven by peripheral and hindbrain glucagon-like-peptide-1 receptor stimulation.

The effects of peripheral glucagon like peptide-1 receptor (GLP-1R) stimulation on feeding, gastric emptying, and energetic responses involve vagal transmission and central nervous system processing. Despite a lack of studies aimed at determining which central nervous system regions are critical for the GLP-1R response production, hypothalamic/forebrain processing is regarded as essential for these effects. Here the contribution of the caudal brainstem to the control of food intake, core temperature, heart rate, and gastric emptying responses generated by peripheral delivery of the GLP-1R agonist, exendin-4 (Ex-4), was assessed by comparing responses of chronic supracollicular decerebrate (CD) rats to those of pair-fed intact control rats. Responses driven by hindbrain intracerebroventricular (fourth icv) delivery of Ex-4 were also evaluated. Intraperitoneal Ex-4 (1.2 and 3.0 μg/kg) suppressed glucose intake in both CD rats (5.0 ± 1.2 and 4.4 ± 1.1 ml ingested) and controls (9.4 ± 1.5 and 7.7 ± 0.8 ml ing...
Complex Challenges in Treating Depression During Pregnancy

The treatment of depression during pregnancy can be challenging for patients and providers alike. An increasing attention to perinatal mood disorders has led to an expanding literature that is often difficult for providers to navigate. It can be a challenge for providers to feel comfortable reviewing the broad scope of the risks and benefits of treatments in the context of the limitations of the literature. Women who are depressed during pregnancy have been found to have an elevated risk of poor obstetrical outcomes, although studies of the relationship between depression and outcomes are limited. Women who are treated with antidepressants during pregnancy are also at risk for a host of poor obstetrical and fetal outcomes. The risks for these outcomes are often confused by confounding factors and study design limitations. Understanding the current data and their limitations will allow providers to guide their patients in choosing treatment options. Consistent and simple strategies should be used when disc...
Current algebra and kaon-nucleon scattering length sum rules

The method of Fubini and Furlan has been used to obtain hard-kaon corrections to the current algebra values for the kaon-nucleon scattering amplitudes at physical threshold. Using the experimental values for the scattering lengths, we have made several predictions on the low-energy kaon-nucleon interactions in the resonance approximation. It is shown that the unsubtracted dispersion relations and superconvergence relations which form the basis of the method are sufficient conditions for yet another derivation of the Adler-Weisberger low-energy theorem.
Comorbidities Drive Outcomes for Both Malignancy-Associated and Non–Malignancy-Associated Hemophagocytic Syndrome

Abstract Background Secondary hemophagocytic syndrome (SHPS) is a syndrome that develops as a result of infection, autoimmunity, or underlying malignancy. We studied novel predictors of mortality among adults with SHPS. Patients and Methods SHPS were identified from the Nationwide Inpatient Sample for 2009 to 2011 using International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM), codes. Charlson comorbidity index (CCI) was used for comorbidity assessment, excluding malignancy. Patient- and hospital-related factors on mortality were assessed by chi-square test or analysis of variance. P values were 2 sided, and the level of significance was .05. Results A total of 276 patient hospitalizations with SHPS were identified. Forty-four had an associated malignancy, 38 (86%) of which were hematologic. Median age was 42 years (range, 18-89 years). A total of 66% (n = 182) had a CCI of 0, 13% (n = 27) had a CCI of 1, and 21% (n = 57) had a CCI of 2 or more. On bivariate analysis, inpatient mortality rate was significantly higher in malignancy-associated hemophagocytic syndrome (HPS) (odds ratio [OR], 2.07; P = .04), age ≥ 50 years (OR, 3.46; P P P P Conclusion Malignancy-associated HPS, CCI ≥ 2, age > 50 years, and Medicare patients were associated with a worse in-hospital mortality. In multivariate analysis, greater comorbidity burden appeared to be the single most important predictor of mortality. This suggests that outcomes for adults with HPS are predicated by the extent of organ dysfunction at diagnosis.
An Evolution of Form and Content: A Practical Guide to Use of the FASB's Conceptual Framework

Equations are only as reliable as we make them. This is true in all disciplines, including accounting. They are forms accommodating content. So, if the balance sheet (A = L OE) and the income statement (R – E = I) equations, for example, structure imprecise business conditions and operations, accountants try to improve their use, not ignore or discard them. The same is true of conceptual frameworks. They are as subject to error or misuse as the balance sheet and income statement equations. Consequently, the accounting profession is not willing to give up on conceptual frameworks, either. Although conceptual frameworks have not been in use as long as, and do not have the same degree of acceptance or understanding as, the income statement and balance sheet, they, too, can be structured to be as useful as the accounting equations. To accomplish this, a conceptual framework’s form is distinguished from its content, similar to distinguishing the form of the balance sheet, A = L OE, from its content. The form and content are then applied to an accounting transaction to demonstrate how to rigorously apply a conceptual framework.
China’s Currency Regime: 2005-2009

The recent changes in the Chinese currency regime are examined by proposing, that due to a misunderstanding, the Chinese government was assumed to be adopting a currency basket, when their announced intention was really a period of “experimentation” that is intended to eventually lead to a managed float regime for the Yuan/renminbi (RMB), tempered by maintaining a certain purchasing power for the RMB. Using new structural breakpoint analysis developed by Qu and Perron (2007) , and robust regression analysis, confirms that there have been six distinct eras of currency policy for the RMB since July of 2005, including reference versus the US dollar, Japanese yen, and the euro that have featured flexible weightings over time. The true regime seems to be one of a currency policy that attempts to balance a more flexible currency with a need to maintain a certain degree of purchasing power and price stability.
Advanced computational methods in multi-view medical imaging

Modern automatic imaging methods can help physicians to visualize physical details in the patient's body. Such methods must be efficient and reliable to allow making the right decisions during clinical intervention. This thesis presents three medical challenges involving multi-view fluoroscopy and proposes corresponding innovative computational methods. The first method addresses challenges of multiple catheter detection and tracking in fluoroscopic guided interventions. The proposed algorithm incorporates the clinical setup constraints and uses a novel computationally efficient geodesic properties framework that traces the catheter from the sheath to the tip. The method was validated on 1107 fluoroscopic images, demonstrating robust multiple catheter tracking. The second method helps avoid serious complications during a cardiac ablation procedure by extracting esophageal silhouettes and reconstructing a 3D model from fluoroscopic views. The thesis describes the key algorithmic components and suggests how the result could help the clinical workflow. The third method presents automatic image-based cardiac and respiratory cycle gating of image sequences. We developed a novel algorithm for an automatic detection of the moving organ directly from images. The algorithm was validated on X-Ray angiographic and intra-cardiac echocardiography images. The method is very fast and its effectiveness was demonstrated on 3D intra-cardiac ultrasound sequences. All three methods are computationally efficient, robust and represent the state-of-the-art of medical imaging challenges.
Forests and Water Yield

Over half a century ago (1897) the Federal Government passed a law that provided for the permanent administration of forest reserves carved out of the rapidly diminishing public domain lands. These forest reserves (now called national forests) were established in part to secure "favorable conditions of water flows." This law was not passed on the basis of facts established by experiments. But, over a long period of time keen observers of nature had developed a concept that forests have a regulatory function upon streamflow. Thus, with only opinions to guide them, our early legislators passed a law which was far-reaching in its effects. Controlled experiments have now verified earlier concepts that streamflow is regulated by forests. And the knowledge gained from numerous experiments conducted both in this country and abroad has led to a new science of water-shed management; a science that will gain in stature as more knowledge is accumulated.
Ceph Distributed File System Benchmarks on an Openstack Cloud

Ceph is a distributed file system that provides high performance, reliability, and scalability. Ceph maximizes the separation between data and metadata management by replacing allocation tables with a pseudo-random data distribution function (CRUSH) designed for heterogeneous and dynamic clusters of unreliable object storage devices (OSDs). In this paper, we investigate the performance of Ceph on an Open Stack cloud using well-known benchmarks. Our results show its good performance and scalability.
Atlantoaxial instability of inflammatory origin in adults: case reports, literature review, and rationale for early surgical intervention.

Background and importance Acquired atlantoaxial instability of inflammatory origin (Grisel syndrome) is a rare condition. It usually occurs in children with benign upper airway problems and responds well to immobilization, rarely requiring C1-2 arthrodesis. Our recent experience with 2 adult cases suggests this may not be true in an older subpopulation. Clinical presentation A 71-year-old man developed C1-2 instability in the setting of culture-negative endocarditis. Initial immobilization was attempted for 8 weeks but new imaging revealed progressive destruction of the odontoid and worsening instability. Symptoms resolved after C1-4 arthrodesis. A 35-year-old woman developed C1-2 instability after a molar extraction and otitis media. Despite 12 weeks of immobilization and antibiotics, symptoms persisted and the atlantodental interval increased. She was successfully treated with a C1-2 arthrodesis. Conclusion A literature review revealed 13 reports (14 cases) of inflammatory atlantoaxial instability in patients aged 18 and older since 1830. Including the 2 cases reported here, 11 cases underwent initial nonoperative treatment with durable satisfactory results in only 2 of them (18.2%). Aspiration of the C1-2 phlegmon was diagnostic in only 4 of these 16 cases. Destruction of the odontoid was seen in a minority of cases (5/16, 31.3%). In this first review of the topic since the introduction of screw-based C1-2 fixation, it is suggested that nonoperative treatment is futile for inflammatory atlantoaxial instability in adults and strong consideration should be given to C1-2 arthrodesis. This procedure can reliably produce good outcomes with minimal morbidity.