bluuebunny/crossref_metadata_2025 huggingface dataset:
Promoter activity dynamics in the lag phase of Escherichia coli
Authors: Madar Daniel , Dekel Erez , Bren Anat , Zimmer Anat , Porat Ziv , Alon Uri
Published: December 2013

Background

Lag phase is a period of time with no growth that occurs when stationary phase bacteria are transferred to a fresh medium. Bacteria in lag phase seem inert: their biomass does not increase. The low number of cells and low metabolic activity make it difficult to study this phase. As a consequence, it has not been studied as thoroughly as other bacterial growth phases. However, lag phase has important implications for bacterial infections and food safety. We asked which, if any, genes are expressed in the lag phase of Escherichia coli, and what is their dynamic expression pattern.

Results

We developed an assay based on imaging flow cytometry of fluorescent reporter cells that overcomes the challenges inherent in studying lag phase. We distinguish between lag1 phase- in which there is no biomass growth, and lag2 phase- in which there is biomass growth but no cell division. We find that in lag1 phase, most promoters are not active, except for the enzymes that utilize the specific carbon source in the medium. These genes show promoter activities that increase exponentially with time, despite the fact that the cells do not measurably increase in size. An oxidative stress promoter, katG, is also active. When cells enter lag2 and begin to grow in size, they switch to a full growth program of promoter activity including ribosomal and metabolic genes.

Conclusions

The observed exponential increase in enzymes for the specific carbon source followed by an abrupt switch to production of general growth genes is a solution of an optimal control model, known as bang-bang control. The present approach contributes to the understanding of lag phase, the least studied of bacterial growth phases.
Giant invasive spinal schwannoma in children: a case report and review of the literature
Authors: Vadivelu Sudhakar , Prasad Prashant , Adesina Adekunle M , Kim Eugene , Luerssen Thomas G , Jea Andrew
Published: December 2013

Introduction

Giant invasive spinal schwannoma is defined as a tumor that extends over two or more vertebral levels, erodes vertebral bodies, and extends into the extraspinal space disrupting myofascial planes. Because of its rarity, there have been few published reports describing clinical features and surgical outcomes, especially in the pediatric patient population.

Case presentation

We analyzed the medical record, pathologic findings, and radiographic studies of a 14-year-old Hispanic boy who presented to Texas Children’s Hospital with a three-month history of progressive spastic paraparesis. Preoperative computed tomography and magnetic resonance imaging reports showed a large mass lesion centered at the left T7-8 neural foramen with intra- and extraspinal extension, resulting in severe spinal cord compression and vertebral body erosion, and protrusion into the retropleural space and descending aorta. Our patient underwent a single-stage posterior approach for complete resection of the tumor with reconstruction and stabilization of the vertebral column. The pathological examination was consistent with schwannoma. At the six-month follow-up, our patient had resolution of preoperative symptoms and remains neurologically intact without any radiographic evidence of recurrent tumor.

Conclusion

To the best of our knowledge, our case represents the fourth child with giant invasive spinal schwannoma reported in the literature. We describe our case and review the literature to discuss the aggregate clinical features, surgical strategies, and operative outcomes for giant invasive spinal schwannoma in the pediatric age group.
Intrathoracic intestinal diverticulum in a late presenting congenital bilateral diaphragmatic hernia: a case report
Authors: Gómez-Rosales Ruth , Petersen-Morfín Santiago , Haro-García Miguel , Ortiz-González Alejandra , Porras-Ruiz Alejandro , González-Chávez Roberto
Published: December 2013

Introduction

Hernias comprise 3% of all defects of the diaphragm. Bilateral hernias are extremely rare and usually occur in children. Here we present a case report of a bilateral Morgagni-Larrey diaphragmatic hernia with an intrathoracic intestinal diverticulum and late presentation. To the best of our knowledge this is the first report of this type.

Case presentation

A 37-year-old Hispanic man was admitted to our emergency department with a 4-day history of obstipation, abdominal pain, distension, nausea, and vomiting. During the initial evaluation, chest and abdominal X-rays were performed, which revealed intestinal displacement into his right and left hemithorax. During laparotomy, a Morgagni-Larrey hernia with a sac was found. His small bowel with a large diverticulum, transverse colon, descending colon, and epiploic fat were herniated into his thorax. Tissues were returned to his abdominal cavity and the hernia defects were corrected with running non-absorbable sutures. He had no postoperative complications.

Conclusions

Bilateral congenital diaphragmatic hernias remain extremely rare. However, they should be considered in adult patients with intestinal obstruction even when respiratory symptoms are absent. This is the first description of a patient with a prolapsed intestinal diverticulum and bilateral diaphragmatic hernias.
Genomic analyses with biofilter 2.0: knowledge driven filtering, annotation, and model development
Authors: Pendergrass Sarah A , Frase Alex , Wallace John , Wolfe Daniel , Katiyar Neerja , Moore Carrie , Ritchie Marylyn D
Published: December 2013

Background

The ever-growing wealth of biological information available through multiple comprehensive database repositories can be leveraged for advanced analysis of data. We have now extensively revised and updated the multi-purpose software tool Biofilter that allows researchers to annotate and/or filter data as well as generate gene-gene interaction models based on existing biological knowledge. Biofilter now has the Library of Knowledge Integration (LOKI), for accessing and integrating existing comprehensive database information, including more flexibility for how ambiguity of gene identifiers are handled. We have also updated the way importance scores for interaction models are generated. In addition, Biofilter 2.0 now works with a range of types and formats of data, including single nucleotide polymorphism (SNP) identifiers, rare variant identifiers, base pair positions, gene symbols, genetic regions, and copy number variant (CNV) location information.

Results

Biofilter provides a convenient single interface for accessing multiple publicly available human genetic data sources that have been compiled in the supporting database of LOKI. Information within LOKI includes genomic locations of SNPs and genes, as well as known relationships among genes and proteins such as interaction pairs, pathways and ontological categories.

Via Biofilter 2.0 researchers can:

•
Annotate
genomic location or region based data, such as results from association studies, or CNV analyses, with relevant biological knowledge for deeper interpretation

•
Filter
genomic location or region based data on biological criteria, such as filtering a series SNPs to retain only SNPs present in specific genes within specific pathways of interest

•
Generate Predictive Models
for gene-gene, SNP-SNP, or CNV-CNV interactions based on biological information, with priority for models to be tested based on biological relevance, thus narrowing the search space and reducing multiple hypothesis-testing.

Conclusions

Biofilter is a software tool that provides a flexible way to use the ever-expanding expert biological knowledge that exists to direct filtering, annotation, and complex predictive model development for elucidating the etiology of complex phenotypic outcomes.
Developing and solving two-echelon inventory system for perishable items in a supply chain: case study (Mashhad Behrouz Company)
Authors: AriaNezhad Mirbahador Gholi , Makuie Ahmad , Khayatmoghadam Saeed
Published: December 2013

In this research, a new two-echelon model has been presented to control the inventory of perishable goods. The performance of the model lies in a supply chain and is based on real conditions and data. The main purpose of the model is to minimize the maintenance cost of the entire chain. However, if the good is perished before reaching the customer (the expiration date is over), the cost would be added to other costs such as transportation, production, and maintenance costs in the target function. As real conditions are required, some limitations such as production time, storage capacity, inventory level, transportation methods, and sustainability time are considered in the model. Also, due to the complexity of the model, the solution approach is based on genetic algorithm under MATLAB to solve and confirm the accuracy of the model’s performance. As can be noted, the manipulation of parametric figures can solve the problem of reaching the optimum point. Using real data from a food production facility, the model was utilized with the same approach and the obtained results confirm the accuracy of the model.
Carprofen inhibits the release of matrix metalloproteinases 1, 3, and 13 in the secretome of an explant model of articular cartilage stimulated with interleukin 1β
Authors: Williams Adam , Smith Julia R , Allaway David , Harris Pat , Liddell Susan , Mobasheri Ali
Published: December 2013

Introduction

Arthritic diseases are characterized by the degradation of collagenous and noncollagenous extracellular matrix (ECM) components in articular cartilage. The increased expression and activity of matrix metalloproteinases (MMPs) is partly responsible for cartilage degradation. This study used proteomics to identify inflammatory proteins and catabolic enzymes released in a serum-free explant model of articular cartilage stimulated with the pro-inflammatory cytokine interleukin 1β (IL-1β). Western blotting was used to quantify the release of selected proteins in the presence or absence of the cyclooxygenase-2 specific nonsteroidal pro-inflammatory drug carprofen.

Methods

Cartilage explant cultures were established by using metacarpophalangeal joints from horses euthanized for purposes other than research. Samples were treated as follows: no treatment (control), IL-1β (10 ng/ml), carprofen (100 μg/ml), and carprofen (100 μg/ml) + IL-1β (10 ng/ml). Explants were incubated (37°C, 5% CO2) over twelve day time courses. High-throughput nano liquid chromatography/mass spectrometry/mass spectrometry uncovered candidate proteins for quantitative western blot analysis. Proteoglycan loss was assessed by using the dimethylmethylene blue (DMMB) assay, which measures the release of sulfated glycosaminoglycans (GAGs).

Results

Mass spectrometry identified MMP-1, -3, -13, and the ECM constituents thrombospondin-1 (TSP-1) and fibronectin-1 (FN1). IL-1β stimulation increased the release of all three MMPs. IL-1β also stimulated the fragmentation of FN1 and increased chondrocyte cell death (as assessed by β-actin release). Addition of carprofen significantly decreased MMP release and the appearance of a 60 kDa fragment of FN1 without causing any detectable cytotoxicity to chondrocytes. DMMB assays suggested that carprofen initially inhibited IL-1β-induced GAG release, but this effect was transient. Overall, during the two time courses, GAG release was 58.67% ± 10.91% (SD) for IL-1β versus 52.91% ± 9.35% (SD) with carprofen + IL-1β.

Conclusions

Carprofen exhibits beneficial anti-inflammatory and anti-catabolic effects in vitro without causing any detectable cytotoxicity. Combining proteomics with this explant model provides a sensitive screening system for anti-inflammatory compounds.
Survival of hematological patients after discharge from the intensive care unit: a prospective observational study
Authors: Bernal Teresa , Pardavila Estefanía V , Bonastre Juan , Jarque Isidro , Borges Marcio , Bargay Joan , Ayestarán Jose Ignacio , Insausti Josu , Marcos Pilar , González-Sanz Victor , Martínez-Camblor Pablo , Albaiceta Guillermo M
Published: December 2013

Introduction

Although the survival rates of hematological patients admitted to the ICU are improving, little is known about the long-term outcome. Our objective was to identify factors related to long-term outcome in hematological patients after ICU discharge.

Methods

A prospective, observational study was carried out in seven centers in Spain. From an initial sample of 161 hematological patients admitted to one of the participating ICUs during the study period, 62 were discharged alive and followed for a median time of 23 (1 to 54) months. Univariate and multivariate analysis were performed to identify the factors related to long term-survival. Finally, variables that influence the continuation of the scheduled therapy for the hematological disease were studied.

Results

Mortality after ICU discharge was 61%, with a median survival of 18 (1 to 54) months. In the multivariate analysis, an Eastern Cooperative Oncology Group score (ECOG) >2 at ICU discharge (Hazard ratio 11.15 (4.626 to 26.872)), relapse of the hematological disease (Hazard ratio 9.738 (3.804 to 24.93)) and discontinuation of the planned treatment for the hematological disease (Hazard ratio 4.349 (1.286 to 14.705)) were independently related to mortality. Absence of stem cell transplantation, high ECOG and high Acute Physiology and Chronic Health Evaluation II (APACHE II) scores decreased the probability of receiving the planned therapy for the hematological malignancy.

Conclusions

Both ICU care and post-ICU management determine the long-term outcome of hematological patients who are discharged alive from the ICU.
Effects of clinically relevant acute hypercapnic and metabolic acidosis on the cardiovascular system: an experimental porcine study
Authors: Stengl Milan , Ledvinova Lenka , Chvojka Jiri , Benes Jan , Jarkovska Dagmar , Holas Jaromir , Soukup Patrik , Sviglerová Jitka , Matejovic Martin
Published: December 2013

Introduction

Hypercapnic acidosis (HCA) that accompanies lung-protective ventilation may be considered permissive (a tolerable side effect), or it may be therapeutic by itself. Cardiovascular effects may contribute to, or limit, the potential therapeutic impact of HCA; therefore, a complex physiological study was performed in healthy pigs to evaluate the systemic and organ-specific circulatory effects of HCA, and to compare them with those of metabolic (eucapnic) acidosis (MAC).

Methods

In anesthetized, mechanically ventilated and instrumented pigs, HCA was induced by increasing the inspired fraction of CO2 (n = 8) and MAC (n = 8) by the infusion of HCl, to reach an arterial plasma pH of 7.1. In the control group (n = 8), the normal plasma pH was maintained throughout the experiment. Hemodynamic parameters, including regional organ hemodynamics, blood gases, and electrocardiograms, were measured in vivo. Subsequently, isometric contractions and membrane potentials were recorded in vitro in the right ventricular trabeculae.

Results

HCA affected both the pulmonary (increase in mean pulmonary arterial pressure (MPAP) and pulmonary vascular resistance (PVR)) and systemic (increase in mean arterial pressure (MAP), decrease in systemic vascular resistance (SVR)) circulations. Although the renal perfusion remained unaffected by any type of acidosis, HCA increased carotid, portal, and, hence, total liver blood flow. MAC influenced the pulmonary circulation only (increase in MPAP and PVR). Both MAC and HCA reduced the stroke volume, which was compensated for by an increase in heart rate to maintain (MAC), or even increase (HCA), the cardiac output. The right ventricular stroke work per minute was increased by both MAC and HCA; however, the left ventricular stroke work was increased by HCA only. In vitro, the trabeculae from the control pigs and pigs with acidosis showed similar contraction force and action-potential duration (APD). Perfusion with an acidic solution decreased the contraction force, whereas APD was not influenced.

Conclusions

MAC preferentially affects the pulmonary circulation, whereas HCA affects the pulmonary, systemic, and regional circulations. The cardiac contractile function was reduced, but the cardiac output was maintained (MAC), or even increased (HCA). The increased ventricular stroke work per minute revealed an increased work demand placed by acidosis on the heart.
Development of Earthquake Energy Demand Spectra
Authors: Dindar Ahmet Anıl , Yalçın Cem , Yüksel Ercan , Özkaynak Hasan , Büyüköztürk Oral
Published: December 2013

Current seismic codes are generally based on the use of response spectra in the computation of the seismic demand of structures. This study evaluates the use of energy concept in the determination of the seismic demand due to its potential to overcome the shortcomings found in the current response spectra–based methods. The emphasis of this study is placed on the computation of the input and plastic energy demand spectra directly derived from the energy-balance equation with respect to selected far-field ground motion obtained from Pacific Earthquake Engineering Research (PEER) database, soil classification according to National Earthquake Hazards Reduction Program (NEHRP) and characteristics of the structural behavior. The concept and methodology are described through extensive nonlinear time history analyses of single-degree-of-freedom (SDOF) systems. The proposed input and plastic energy demand spectra incorporate different soil types, elastic perfectly plastic constitutive model, 5% viscous damping ratio, different ductility levels, and varying seismic intensities.
A SSHAC Level 3 Probabilistic Seismic Hazard Analysis for a New-Build Nuclear Site in South Africa
Authors: Bommer Julian J. , Coppersmith Kevin J. , Coppersmith Ryan T. , Hanson Kathryn L. , Mangongolo Azangi , Neveling Johann , Rathje Ellen M. , Rodriguez-Marek Adrian , Scherbaum Frank , Shelembe Refilwe , Stafford Peter J. , Strasser Fleur O.
Published: December 2013

A probabilistic seismic hazard analysis has been conducted for a potential nuclear power plant site on the coast of South Africa, a country of low-to-moderate seismicity. The hazard study was conducted as a SSHAC Level 3 process, the first application of this approach outside North America. Extensive geological investigations identified five fault sources with a non-zero probability of being seismogenic. Five area sources were defined for distributed seismicity, the least active being the host zone for which the low recurrence rates for earthquakes were substantiated through investigations of historical seismicity. Empirical ground-motion prediction equations were adjusted to a horizon within the bedrock at the site using kappa values inferred from weak-motion analyses. These adjusted models were then scaled to create new equations capturing the range of epistemic uncertainty in this region with no strong motion recordings. Surface motions were obtained by convolving the bedrock motions with site amplification functions calculated using measured shear-wave velocity profiles.
Significance of Rotating Ground Motions on Behavior of Symmetric- and Asymmetric-Plan Structures: Part I. Single-Story Structures
Authors: Reyes Juan C. , Kalkan Erol
Published: December 2013

The California Building Code requires at least two ground motion components for the three-dimensional (3-D) response history analysis (RHA) of structures. For near-fault sites, these records should be rotated to fault-normal/fault-parallel (FN/FP) directions, and two RHA analyses should be performed separately. This approach is assumed to lead to two sets of responses that envelope the range of possible responses over all non-redundant rotation angles. This assumption is examined here using 3-D computer models of single-story structures having symmetric and asymmetric plans subjected to a suite of bidirectional earthquake ground motions. The influence that the rotation angle has on several engineering demand parameters is investigated in linear and nonlinear domains to evaluate the use of the FN/FP directions, and the maximum direction (MD). The statistical evaluation suggests that RHAs should be conducted by rotating a set of records to the MD and FN/FP directions, and taking the maximum response values from these analyses as design values.
Displacement-Based Seismic Design for Reinforced Masonry Shear-Wall Structures, Part 1: Background and Trial Application
Authors: Ahmadi Farhad , Mavros Marios , Klingner Richard E. , Shing Benson , McLean David
Published: December 2013

In this paper, a displacement-based seismic design procedure is presented for reinforced masonry shear-wall structures, with the objective of being more consistent, transparent, and practical than current force-based seismic design procedures. The procedure anticipates the formation of a plastic mechanism at specified target displacements, calculates the local deformation demands associated with that mechanism, and ensures that those local deformation demands remain below deformation capacities for flexure-dominated and shear-dominated wall segments. Guidelines to determine the target displacements and effective damping properties for reinforced masonry wall structures are provided. The proposed procedure and guidelines are used in a trial application to design a full-scale, two-story reinforced masonry shear-wall system.
Loss Estimation of Tall Buildings Designed for the PEER Tall Building Initiative Project
Authors: Shome Nilesh , Jayaram Nirmal , Krawinkler Helmut , Rahnama Mohsen
Published: December 2013

As part of the PEER Center's Tall Building Initiative (TBI) project, practicing engineers designed three structural systems, each based on commonly used codes and guidelines, in addition to the guidelines developed by PEER. The designs were analyzed by three research teams, using a set of 75 ground-motion pairs, to predict response parameters for evaluating the performance of tall buildings. This study focuses on analytically estimating the seismic losses to these buildings to assess their relative seismic performance. The loss assessment process follows a comprehensive simulation approach that takes into account several random variables, such as building response, repair costs, etc. Throughout this study, epistemic and aleatory uncertainties in the random variables are accounted for in order to quantify those in loss estimates. Based on the dollar-loss results, the performance of the dual-system building is compared and contrasted with that of the other building systems considered in the PEER study.
Mass Spectrometry in Russia
Authors: Zaikin Vladimir G. , Sysoev Alexander A.
Published: December 2013

The present review covers the main research in the area of mass spectrometry from the 1990s which was about the same time as the Russian Federation emerged from the collapse of the Soviet Union (USSR). It consists of two main parts—application of mass spectrometry to chemistry and related fields and creation and development of mass spectrometric technique. Both traditional and comparatively new mass spectrometric methods were used to solve various problems in organic chemistry (reactivity of gas-phase ions, structure elucidation and problems of identification, quantitative and trace analysis, differentiation of stereoisomers, derivatization approaches etc.), biochemistry (proteomics and peptidomics, lipidomics), medical chemistry (mainly the search of biomarkers, pharmacology, doping control), environmental, petrochemistry, polymer chemistry, inorganic and physical chemistry, determination of natural isotope ratio etc. Although a lot of talented mass spectrometrists left Russia and moved abroad after the collapse of the Soviet Union, the vitality of the mass spectral community proved to be rather high, which allowed the continuation of new developments in the field of mass spectrometric instrumentation. They are devoted to improvements in traditional magnetic sector mass spectrometers and the development of new ion source types, to analysis and modification of quadrupole, time-of-flight (ToF) and ion cyclotron resonance (ICR) analyzers. The most important achievements are due to the creation of multi-reflecting ToF mass analyzers. Special attention was paid to the construction of compact mass spectrometers, particularly for space exploration, of combined instruments, such as ion mobility spectrometer/mass spectrometer and accelerating mass spectrometers. The comparatively young Russian Mass Spectrometry Society is working hard to consolidate the mass spectrometrists from Russia and foreign countries, to train young professionals on new appliances and regularly holds conferences on mass spectrometry. For ten years, a special journal Mass-spektrometria has published papers on all disciplines of mass spectrometry.
Study of Challenging Calcium Alkoxides in Solution by Electrospray Ionisation Mass Spectrometry (Part 2)
Authors: Peruzzo Valentina , Chiurato Matteo Andrea , Tomasin Patrizia , Brianese Nicola , Traldi Pietro , Favaro Monica
Published: December 2013

Calcium alkoxides in solution give rise to oligomers with different reactivity and solubility and, as observed in a previous investigation, small differences in the ligand structure lead to strong differences in the cluster composition. Electrospray ionisation mass spectrometry (ESI-MS) gives evidence of this behaviour, allowing the identification of these oligomers. In this paper, ESI was applied in the study of calcium alkoxides with different steric hindrances and with additional donor atoms on the ligands. A systematic analysis was conducted by varying the ESI instrumental parameters (voltages, temperatures) to identify the best conditions for the analysis of this class of compounds. Furthermore, particular attention was paid to the study of the best solvent to be employed, considering the possible occurrence of alcoholysis and decomplexation phenomena.
Mass Spectrometry as an Efficient Tool for the Characterization of Amyloid β Peptide 25–35 Self-Assembly Species in Aggregation and Inhibition Studies
Authors: Fiori J. , Naldi M. , Andrisano V.
Published: December 2013

Amyloid beta 25–35 [Aβ (25–35)], as a peptide model for full-length Aβ in structural and functional investigations, has been chosen for aggregation studies. The complexity of the Aβ (25–35) aggregation process required a multi-methodological analytical approach to obtain reliable and reproducible results. Here, we describe the results obtained by the use of mass spectrometry (MS) for the structural characterization of the self-assembly species during the aggregation process and for the definition of the self-assembly kinetics and myricetin inhibition patterns, comparing the results with those obtained by using the well-established spectroscopic method based on thioflavin T fluorescence. Flow injection electrospray ionization-ion trap-mass spectrometry (ESI-IT-MS) was applied to monitor the disappearance of the monomer specie in the first steps, whereas matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-ToF-MS) was used to follow monomer and small oligomer self-assembly trends in the early stages of the nucleating process.
A Fast and Validated Mass Spectrometry Method for the Evaluation of Human Serum Albumin Structural Modifications in the Clinical Field
Authors: Naldi M. , Giannone F.A. , Baldassarre M. , Domenicali M. , Caraceni P. , Bernardi M. , Bertucci C.
Published: December 2013

A relatively fast analytical method for the identification and quantification of the post-transcriptional changes (PTCs) occurring in circulating human serum albumin (HSA) was developed. HSA is the most abundant protein in plasma and it represents the main determinant of plasma oncotic pressure, thus being the main modulator of fluid distribution between body compartments. Cirrhotic patients have low levels of HSA. Moreover, recent studies have demonstrated that during liver cirrhosis HSA presents PTCs affecting its properties. The HSA isoforms derived from these modifications could represent promising biomarkers for liver disease. Human plasma samples were collected from a cirrhotic patient (CH) and from an aged-matched non-cirrhotic subject (CT), purified by reverse-phase chromatography and analysed by an electrospray ionization quadrupole time-of-flight (ESI-Q-ToF) spectrometer. The deconvoluted ESI mass spectra from healthy subjects were all characterized by peaks attributed to mercaptoalbumin, nitrosylated, cysteinylated, glycated and N-terminal truncated HSA isoforms. The relative abundance of each isoform was derived and transformed into a relative per cent amount and the results were compared to those obtained analysing HSA from a CH plasma. The method was validated in terms of intra-day and inter-day reproducibility, both for quantitative results and PTCs molecular weight determination. The optimized method resulted in being effective in disclosing changes in HSA isoforms relative abundance and then it could be used for the systematic screening of cirrhotic patients to identify promising new biomarkers for liver diseases.
JSim, an open-source modeling system for data analysis
Authors: Butterworth Erik , Jardine Bartholomew E. , Raymond Gary M. , Neal Maxwell L. , Bassingthwaighte James B.
Published: December 2013

JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological and pharmacological systems through the testing of model solutions against data. It is designed for interactive, iterative manipulation of the model code, handling of multiple data sets and parameter sets, and for making comparisons among different models running simultaneously or separately. Interactive use is supported by a large collection of graphical user interfaces for model writing and compilation diagnostics, defining input functions, model runs, selection of algorithms solving ordinary and partial differential equations, run-time multidimensional graphics, parameter optimization (8 methods), sensitivity analysis, and Monte Carlo simulation for defining confidence ranges. JSim uses Mathematical Modeling Language (MML) a declarative syntax specifying algebraic and differential equations. Imperative constructs written in other languages (MATLAB, FORTRAN, C++, etc.) are accessed through procedure calls. MML syntax is simple, basically defining the parameters and variables, then writing the equations in a straightforward, easily read and understood mathematical form. This makes JSim good for teaching modeling as well as for model analysis for research.   For high throughput applications, JSim can be run as a batch job.  JSim can automatically translate models from the repositories for Systems Biology Markup Language (SBML) and CellML models. Stochastic modeling is supported. MML supports assigning physical units to constants and variables and automates checking dimensional balance as the first step in verification testing. Automatic unit scaling follows, e.g. seconds to minutes, if needed. The JSim Project File sets a standard for reproducible modeling analysis: it includes in one file everything for analyzing a set of experiments: the data, the models, the data fitting, and evaluation of parameter confidence ranges. JSim is open source; it and about 400 human readable open source physiological/biophysical models are available at http://www.physiome.org/jsim/.
Altered functional connectivity in posttraumatic stress disorder with versus without comorbid major depressive disorder: a resting state fMRI study
Authors: Kennis Mitzy , Rademaker Arthur R. , van Rooij Sanne J.H. , Kahn René S. , Geuze Elbert
Published: December 2013

Posttraumatic stress disorder (PTSD) is an anxiety disorder that is often diagnosed with comorbid depressive disorder. Therefore, neuroimaging studies investigating PTSD typically include both patients with and without comorbid depression. Differences in activity of the anterior cingulate cortex (ACC) and insula have been shown to differentiate PTSD patients with and without major depressive disorder (MDD). Whether or not comorbid MDD affects resting state functional connectivity of PTSD patients has not been investigated to our knowledge. Here, resting state functional connectivity of PTSD patients with (PTSD+MDD; n=27) and without (PTSD-MDD; n=23) comorbid MDD was investigated. The subgenual ACC and insula were investigated as seed regions. Connectivity between the subgenual ACC and perigenual parts of the ACC was increased in PTSD+MDD versus PTSD-MDD. Reduced functional connectivity of the subgenual ACC with the thalamus was found in the PTSD+MDD group versus the PTSD-MDD group. These results remained significant after controlling for PTSD severity. In addition, the PTSD+MDD group showed reduced functional connectivity of the insula with the hippocampus compared to the PTSD-MDD group. However, this cluster was no longer significantly different when controlling for PTSD severity. Thus, resting state functional connectivity of the subgenual ACC may distinguish PTSD+MDD from PTSD-MDD. As PTSD patients with comorbid MDD are more treatment resistant, this result may be important for treatment development.
Improving Health Outcomes Through Better Capacity Allocation in a Community-Based Chronic Care Model
Authors: Deo Sarang , Iravani Seyed , Jiang Tingting , Smilowitz Karen , Samuelson Stephen
Published: December 2013

This paper studies a model of community-based healthcare delivery for a chronic disease. In this setting, patients periodically visit the healthcare delivery system, which influences their disease progression and consequently their health outcomes. We investigate how the provider can maximize community-level health outcomes through better operational decisions pertaining to capacity allocation across different patients. To do so, we develop an integrated capacity allocation model that incorporates clinical (disease progression) and operational (capacity constraint) aspects. Specifically, we model the provider's problem as a finite horizon stochastic dynamic program, where the provider decides which patients to schedule at the beginning of each period. Therapy is provided to scheduled patients, which may improve their health states. Patients that are not seen follow their natural disease progression. We derive a quantitative measure for comparison of patients' health states and use it to design an easy-to-implement myopic heuristic that is provably optimal in special cases of the problem. We employ the myopic heuristic in a more general setting and test its performance using operational and clinical data obtained from Mobile C.A.R.E. Foundation, a community-based provider of pediatric asthma care in Chicago. Our extensive computational experiments suggest that the myopic heuristic can improve the health gains at the community level by up to 15% over the current policy. The benefit is driven by the ability of our myopic heuristic to alter the duration between visits for patients with different health states depending on the tightness of the capacity and the health states of the entire patient population.
Optimal Rate Scheduling via Utility-Maximization for J-User MIMO Markov Fading Wireless Channels with Cooperation
Authors: Dai Wanyang
Published: December 2013

We design a dynamic rate scheduling policy of Markov type by using the solution (a social optimal Nash equilibrium point) to a utility-maximization problem over a randomly evolving capacity set for a stochastic system of generalized processor-sharing queues in a random environment whose job arrivals to each queue follow a doubly stochastic renewal process (DSRP). Both the random environment and the random arrival rate of each DSRP are driven by a finite state continuous time Markov chain. The scheduling policy optimizes in a greedy fashion with respect to each queue and environmental state. Since the closed-form solution for the performance of such a queuing system under the policy is difficult to obtain, we establish a reflecting diffusion with regime-switching model for its measures of performance. Furthermore, we justify its asymptotic optimality by deriving the stochastic fluid and diffusion limits for the corresponding system under heavy traffic. In addition, we identify a cost function related to the utility function, which is minimized by minimizing the workload process in the diffusion limit. More importantly, our queuing model includes typical systems in the future wireless networks, such as the J-user multi-input multioutput multiple access channel and the broadcast channel under Markov fading with cooperation and admission control as special cases.
Open Collaboration for Innovation: Principles and Performance
Authors: Levine Sheen S. , Prietula Michael J.
Published: December 2013

The principles of open collaboration for innovation (and production), once distinctive to open source software, are now found in many other ventures. Some of these ventures are Internet based: for example, Wikipedia and online communities. Others are off-line: they are found in medicine, science, and everyday life. Such ventures have been affecting traditional firms and may represent a new organizational form. Despite the impact of such ventures, their operating principles and performance are not well understood. Here we define open collaboration (OC), the underlying set of principles, and propose that it is a robust engine for innovation and production. First, we review multiple OC ventures and identify four defining principles. In all instances, participants create goods and services of economic value, they exchange and reuse each other’s work, they labor purposefully with just loose coordination, and they permit anyone to contribute and consume. These principles distinguish OC from other organizational forms, such as firms or cooperatives. Next, we turn to performance. To understand the performance of OC, we develop a computational model, combining innovation theory with recent evidence on human cooperation. We identify and investigate three elements that affect performance: the cooperativeness of participants, the diversity of their needs, and the degree to which the goods are rival (subtractable). Through computational experiments, we find that OC performs well even in seemingly harsh environments: when cooperators are a minority, free riders are present, diversity is lacking, or goods are rival. We conclude that OC is viable and likely to expand into new domains. The findings also inform the discussion on new organizational forms, collaborative and communal.
What Happens When Evaluation Goes Online? Exploring Apparatuses of Valuation in the Travel Sector
Authors: Orlikowski Wanda J. , Scott Susan V.
Published: December 2013

Our research focuses on the fast-changing landscape of contemporary social media where user-generated content is increasingly being used to evaluate a wide range of products and services. The move to online valuations is raising important questions about how valuations change when they are produced online by consumers and what outcomes they generate for the organizations being evaluated. To address these questions, we investigate two prominent hotel valuation schemes currently at work in the hospitality industry, and we identify significant differences in their valuation practices and outcomes. We develop a practice-based lens for examining the materiality of valuations, providing a way of understanding the differences we observed in terms of performativity. This lens explains both how valuations are actively produced in ongoing practice and how their production is significantly reconfiguring everyday practices of the organizations being evaluated. We conclude by considering the implications of our findings for research on valuation and organizations.
Menopausal Hormone Therapy and Cardiovascular Disease Risk: Utility of Biomarkers and Clinical Factors for Risk Stratification
Authors: Bassuk Shari S , Manson JoAnn E
Published: December 2013

BACKGROUND

Menopausal hormone therapy (HT) continues to have a clinical role in symptom management, but identifying women for whom benefits will outweigh the risks remains a challenge. Although hormone therapy (HT) is the most effective strategy for ameliorating vasomotor and other symptoms, randomized clinical trials show an unfavorable balance of benefits and risks for many women. However, closer examination of data from these trials suggests that it may be possible to classify women as better or worse candidates for HT by using individual risk stratification.

CONTENT

Data from 2 landmark trials—the Women's Health Initiative (WHI) and the Heart and Estrogen/progestin Replacement Study (HERS)—suggest an important role for clinical characteristics, serum biomarkers, genomic markers, and gene–environment interactions in developing a personalized approach to the prediction of risk for cardiovascular disease (CVD) events for women while on HT. The available data suggest several characteristics of women who are optimal candidates for HT use: younger age (<60 years), recent onset of menopause (<10 years), favorable lipid profile (LDL cholesterol <130 mg/dL or LDL/HDL cholesterol ratio <2.5), absence of metabolic syndrome, and absence of factor V Leiden genotype. The identification of other characteristics is an area of active investigation. In addition, women at high risk for venous thromboembolism should avoid systemic HT or choose a transdermal rather than oral delivery route.

Personalized medicine—i.e., the use of the specific biological profile of an individual to guide the choice of treatment—is highly relevant for clinical decision-making regarding HT and offers promise for improved treatment efficacy and safety.
Critical thinking; issues in nursing education and practice
Authors: Aagbedia Clara Oniovokoyubu , Ogbe Joseph
Published: December 2013

The emphasis on the use of the nursing process in both nursing education and clinical practice would lead one to expect that the process of critical thinking is well understood and applied in nursing situation.  But this is not the case.  There is a substantial body of evidence to show that tasks, ward routines and rituals and procedures socialization of neophytes in nursing are strong obstacles to use of critical thinking skills in nursing. Rapid technological changes and increase consumer demand for health services dictate the need for professionally prepared nurses who are competent and capable of critical thinking abilities to process complex data and make and intelligent decision. But the question is, is nursing education and practice promoting critical thinking? This paper examines critical thinking in relation to other modes of thinking used by clinical nurses and issues in providing quality nursing care. In addition, thought processes that can influence nurse’s ability to provide safe, high-quality care are explored. The importance of exploring these thought process is to offer the reader a context in which to judge the appropriateness of nursing actions. Implications to nursing are discussed.   Keywords: Critical thinking, nursing, disposition to critical thinking, evidence-based practice, uncertainty in nursing.
Name-Letters and Birthday-Numbers: Implicit Egotism Effects in Pricing
Authors: Coulter Keith S. , Grewal Dhruv
Published: December 2013

This research examines how the implicit egotism resulting from consumers’ positive self-associations affects their evaluations of product prices. The effects can occur when the product's price and the consumer share either name-letters (name-letter/price effect) or birthday-numbers (birthday-number/price effect). Through a series of studies, the authors demonstrate that the positive affect linked to name-letters and birthday-numbers transfers directly to consumers’ price predilections and ultimately affects their purchase intentions. More specifically, consumers like prices (e.g., “fifty-five dollars”) that contain digits beginning with the same first letter (e.g., “F”) as their own name (e.g., “Fred,” “Mr. Frank”) more than prices that do not. Similarly, prices that contain cents digits (e.g., $49.15) that correspond to a consumer's date of birth (e.g., April 15) also enhance pricing liking and purchase intentions. Across groups of consumers, the authors’ findings demonstrate that implicit egotism effects can result in greater purchase intentions for a higher-priced product compared with a lower-priced product.
Limited Availability Reduces the Rate of Satiation
Authors: Sevilla Julio , Redden Joseph P.
Published: December 2013

In general, consumers enjoy products less with repeated consumption. Unfortunately, there are few known ways to slow such satiation. The authors show that consumers satiate more slowly on a product when it is available for consumption only at limited times. Specifically, they find that perceived limited availability made a product more enjoyable, and yet this effect largely emerged only after repeated consumption. The authors attribute this finding to an urge to take advantage of a rare consumption opportunity, which leads people to pay less attention to the quantity consumed and subsequently to experience less satiation. A series of studies establish the effect of perceived limited availability on the rate of satiation, show that it influences how much people eat, provide mediation evidence of the proposed theoretical account, and eliminate the effect by making salient the total amount consumed. The authors conclude with implications of these findings.
Evaluating questions in journalism
Authors: Lukin Annabelle
Published: December 2013

To evaluate current affairs interviews, an analysis of question types is central. This paper takes data from The 7.30 Report, a current affairs programme broadcast by the Australian Broadcasting Corporation; specifically, interviews with a nightly panel of ‘military experts’ during the 2003 invasion of Iraq by ‘Coalition’ forces. The paper considers how the professional practice of the programme's presenter, a high profile, experienced, Australian journalist (Kerry O'Brien), fulfilled his role at this ‘critical moment’ in the history of Australia's public broadcaster. Drawing on Hasan's metafunctional description of the semantics of questions (Hasan 1983, 1996, in press), the paper presents some evidence that O'Brien's questions allowed the panelists, at least two of whom could not be considered independent, disinterested observers, to construe events largely on their own terms. The multidimensional analysis of O'Brien's questions, which Hasan's message semantic network description enables, brings out various kinds of evidence (interpersonal, ideational and textual) from which it is possible to argue that O'Brien's interviews with this panel constituted a mode of news which served the interests of the belligerent countries.
A pedagogic and professional Case Study genre and register continuum in Business and in Medicine
Authors: Gardner Sheena
Published: December 2013

When students write Case Study assignments at university, they face the demands of the academy and of the profession. This paper explores the choices successful students of Business and Medicine make to meet these competing demands at the levels of genre, register and language. In Case Study genres individual cases, such as a specific company or a patient, are analysed using frameworks accepted within the relevant disciplines. In our classification (Gardner and Nesi 2013), which was developed through analysis of the British Academic Written English (BAWE) corpus of successful student writing, Case Study genres also include a recommendation stage. This paper identifies five genres along a pedagogic to professional continuum. It shows how their registers are shaped by the institutional practices of the discipline (Field), by the competing student and professional roles of the writer (Tenor) and by the action orientation of the text (Mode). Wordings of recommendations retrieved through corpus analysis and interpreted from Systemic Functional Linguistic perspectives as choices within systems bring to light the multifaceted nature of recommendations, as well as disciplinary differences in their prosody and ownership. This study will be of interest to those involved in teaching academic writing, as well as those seeking to understand how professional roles and contexts are construed in texts.