bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polynomial algebra of discrete models in systems biology
Authors: Veliz-Cuba Alan , Jarrah Abdul Salam , Laubenbacher Reinhard 
Published: May 2010

Abstract
Motivation: An increasing number of discrete mathematical models are being published in Systems Biology, ranging from Boolean network models to logical models and Petri nets. They are used to model a variety of biochemical networks, such as metabolic networks, gene regulatory networks and signal transduction networks. There is increasing evidence that such models can capture key dynamic features of biological networks and can be used successfully for hypothesis generation.
Results: This article provides a unified framework that can aid the mathematical analysis of Boolean network models, logical models and Petri nets. They can be represented as polynomial dynamical systems, which allows the use of a variety of mathematical tools from computer algebra for their analysis. Algorithms are presented for the translation into polynomial dynamical systems. Examples are given of how polynomial algebra can be used for the model analysis.
Contact: alanavc@vt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Interest Group Theory
Authors: McFarland Andrew 
Published: May 2010

AbstractThis article considers the four steps of interest group theory as it applies to American politics: group theory; Robert Dahl's pluralism; multiple elitist theory; and neopluralism. Participation in interest groups is seen to be one of four standard modes of participation in American politics. The interest group in niche theory is viewed in the context of other similar interest groups and its competition with them for resources of money and membership for group maintenance. It also pertains to group resource mobilization and group maintenance. The theory of internal democracy is also elaborated upon. Political scientists should keep remembering that attention must be paid to the role of interest groups in the theory and practice of democracy in America.
Evolution of the Eleusine Subgroup of Pyricularia oryzae Inferred from Rearrangement at the Pwl1 Locus (Retracted)
Authors: Tanaka Masaki , Hyon Gang-Su , Murata Toshiki , Nakayashiki Hitoshi , Tosa Yukio 
Published: May 2010

The authors of Tanaka et al. 23:771-783 (2010) retracted this article because it proved to contain a pair of identical images that were used to represent different treatments in Figure 2A. This article was retracted on 3 June 2015. This article was resubmitted.
Long-term Effect of Sciatic Nerve Block with Slow-release Lidocaine in a Rat Model of Postoperative Pain
Authors: Tobe Masaru , Obata Hideaki , Suto Takashi , Yokoo Hideaki , Nakazato Yoichi , Tabata Yasuhiko , Saito Shigeru 
Published: May 2010

Background
Postoperative pain management is important for preventing perioperative complications. The authors examined the effectiveness of controlled-release lidocaine for sciatic nerve block in a rat model of postoperative pain.

Methods
The authors created a novel slow-release lidocaine sheet (SRLS) with polylactic-coglycolic acid. In male Sprague-Dawley rats (postoperative pain model), the authors applied the SRLS, lidocaine alone, or polylactic-coglycolic acid (control) near the ipsilateral sciatic nerve just before making the paw incision. Mechanical hypersensitivity was assessed using von Frey filaments, and c-fos expression was examined in the spinal cord dorsal horn at segments L4-L5. Neurotoxicity and muscle toxicity were also evaluated via histopathology.

Results
The SRLS (30%, w/w) continuously released lidocaine for 1 week in vitro. The withdrawal threshold in the SRLS-treated group was higher than that in the control group at all time points measured (2 h to 7 days). The withdrawal threshold in the lidocaine-treated group was higher than that in the control group only at 2 h after paw incision. The mean number of c-fos immunoreactive neurons in the SRLS-treated group was lower than in the control group at 2, 5, and 48 h after paw incision and lower than in the lidocaine-treated group at 5 and 48 h after paw incision. On histopathology, signs of inflammation were only slightly present in the muscle and nerve tissues of the SRLS-treated group.

Conclusions
Single treatment with the SRLS inhibited hyperalgesia and c-fos expression in the spinal cord dorsal horn for 1 week. Slow-release local anesthetics are promising for the management of postoperative pain.
Modeling the Non–Steady State Respiratory Effects of Remifentanil in Awake and Propofol-sedated Healthy Volunteers
Authors: Olofsen Erik , Boom Merel , Nieuwenhuijs Diederik , Sarton Elise , Teppema Luc , Aarts Leon , Dahan Albert 
Published: May 2010

Background
Few studies address the dynamic effect of opioids on respiration. Models with intact feedback control of carbon dioxide on ventilation (non-steady-state models) that correctly incorporate the complex interaction among drug concentration, end-tidal partial pressure of carbon dioxide concentration, and ventilation yield reliable descriptions and predictions of the behavior of opioids. The authors measured the effect of remifentanil on respiration and developed a model of remifentanil-induced respiratory depression.

Methods
Ten male healthy volunteers received remifentanil infusions with different infusion speeds (target concentrations: 4-9 ng/ml; at infusion rates: 0.17-9 ng x ml x min) while awake and at the background of low-dose propofol. The data were analyzed with a nonlinear model consisting of two additive linear parts, one describing the depressant effect of remifentanil and the other describing the stimulatory effect of carbon dioxide on ventilation.

Results
The model adequately described the data including the occurrence of apnea. Most important model parameters were as follows: C50 for respiratory depression 1.6 +/- 0.03 ng/ml, gain of the respiratory controller (G) 0.42 - 0.1 l x min x Torr, and remifentanil blood effect site equilibration half-life (t(1/2)ke0) 0.53 +/- 0.2 min. Propofol caused a 20-50% reduction of C50 and G but had no effect on t(1/2)ke0. Apnea occurred during propofol infusion only. A simulation study revealed an increase in apnea duration at infusion speeds of 2.5-0.5 ng x ml x min followed by a reduction. At an infusion speed of < or = 0.31 ng x ml x min, no apnea was seen.

Conclusions
The effect of varying remifentanil infusions with and without a background of low-dose propofol on ventilation and end-tidal partial pressure of carbon dioxide concentration was described successfully using a non-steady-state model of the ventilatory control system. The model allows meaningful simulations and predictions.
Dropouts of the outer electron radiation belt in response to solar wind stream interfaces: global positioning system observations
Authors: Morley Steven K. , Friedel Reiner H. W. , Spanswick Emma L. , Reeves Geoffrey D. , Steinberg John T. , Koller Josef , Cayton Thomas , Noveroske Evan 
Published: May 2010

We present a statistical study of relativistic electron counts in the electron radiation belt across a range of drift shells (L*>4) combining data from nine combined X-ray dosimeters (CXD) on the global positioning system (GPS) constellation. The response of the electron counts as functions of time, energy and drift shell are examined statistically for 67 solar wind stream interfaces (SIs); two-dimensional superposed epoch analysis is performed with the CXD data. For these epochs we study the radiation belt dropouts and concurrent variations in key geophysical parameters.
At higher L* we observe a tendency for a gradual drop in the electron counts over the day preceding the SI, consistent with outward diffusion and magnetopause shadowing. At all L*, dropouts occur with a median time scale of ≃7 h and median counts fall by 0.4–1.8 orders of magnitude. The central tendencies of radiation belt dropout and recovery depend on both L* and energy. For ≃70 per cent of epochs Sym-H more than −30 nT, yet only three of 67 SIs did not have an associated dropout in the electron data. Statistical maps of electron precipitation suggest that chorus-driven relativistic electron microbursts might be major contributors to radiation belt losses under high-speed stream driving.
The epidemiology of pure and comorbid generalized anxiety disorder: a review and evaluation of recent research
Authors: Kessler R. C. 
Published: May 2010

Objective: Research documenting high rates of comorbidity among patients with generalized anxiety disorder (GAD) has led to the suggestion that GAD might best be conceptualized as a prodrome, residual or severity marker of other disorders. Recent research investigating this suggestion is reviewed in this report. Method: A computer search cross‐classified the terms ‘Generalized Anxiety’ and ‘Comorbidity’. Results: Results arguing that GAD is an independent disorder include the finding that GAD is usually temporally primary in cases of comorbidity with major depression, that primary GAD is a significant predictor of subsequent depression and that the course of GAD is independent of comorbidity. Studies in both patient and community samples show that the impairment associated with pure GAD is equivalent to the impairment associated with pure depression. Conclusion: The results reviewed here support the view that GAD as an independent disorder is a major public health problem.
Improved survival for relapsed diffuse large B cell lymphoma is predicted by a negative pre‐transplant FDG‐PET scan following salvage chemotherapy
Authors: Dickinson Michael , Hoyt Rosemary , Roberts Andrew W. , Grigg Andrew , Seymour John F. , Prince H. Miles , Szer Jeff , Ritchie David 
Published: May 2010

SummaryThe utility of [18F]fluoro‐2‐deoxy‐ d‐glucose positron‐emission tomography (FDG‐PET) for predicting outcome after autologous stem cell transplantation (ASCT) for diffuse large B cell lymphoma (DLBCL) is uncertain – existing studies include a range of histological subtypes or have a limited duration of follow‐up. Thirty‐nine patients with primary‐refractory or relapsed DLBCL with pre‐ASCT PET scans were analysed. The median follow‐up was 3 years. The 3‐year progression‐free survival (PFS) for patients with positive PET scans pre‐ASCT was 35% vs. 81% for those who had negative PET scans (P = 0·003). The overall survival (OS) in these groups was 39% and 81% (P = 0·01), respectively. In a multivariate analysis, PET result, number of salvage cycles and the presence of relapsed or refractory disease were shown to predict a longer PFS; PET negativity (P = 0·04) was predictive of a longer OS. PET is useful for defining those with an excellent prognosis post‐ASCT. Although those with positive scans can still be salvaged with current treatments, PET may useful for selecting patients eligible for novel consolidation strategies after salvage therapies.
Activation of signal transducer and activator of transcription-1 (STAT-1) and differential expression of interferon-γ and anti-inflammatory proteins in pelvic ileal pouches for ulcerative colitis and familial adenomatous polyposis
Authors: Leal R F , Ayrizono M L S , Milanski M , Coope A , Fagundes J J , Velloso L A , Coy C S R 
Published: May 2010

Summary
Pouchitis after total rectocolectomy is the most common complication of ulcerative colitis (UC). The immunological mechanisms involved in the genesis of pouchitis are unclear. Therefore, we evaluated the inflammatory activity in normal ileal pouch mucosa by determining signal transducers and activators of transcription (STAT-1) activation and cytokine expression in patients operated for UC and familial adenomatous polyposis (FAP). Eighteen asymptomatic patients, who underwent total rectocolectomy and J pouch, were evaluated: nine with UC and nine with FAP. The activation of STAT-1 and cytokine expression were determined by immunoblot of total protein extracts from pouch mucosal biopsies. The absence of pouchitis was assessed by clinical, histological and endoscopic parameters, according to the Pouchitis Disease Activity Index. The patients were not receiving any medication. Analysis of variance (anova) and Tukey–Kramer's test were applied. The local ethical committee approved the study and informed consent was signed by all participants. STAT-1 activation was increased in UC when compared to FAP and controls (P &lt; 0·05). Higher levels of interferon (IFN)-γ expression were observed in UC patients when compared to the control group (P &lt; 0·05), but were similar to FAP. In contrast, cytokine signalling (SOCS-3) and interleukin (IL)-10 expression were similar in all groups (P &gt; 0·05). These findings could explain the higher susceptibility to this inflammatory complication in UC when compared to FAP. A tendency towards increased levels of IFN-γ and STAT-1 in patients with UC, even without clinical and endoscopic evidence of pouchitis, was observed; studying inflammatory activity in asymptomatic ileal pouches may help understanding of the pathogenesis of pouchitis.
Coupled regulation of interleukin-12 receptor beta-1 of CD8+ central memory and CCR7-negative memory T cells in an early alloimmunity in liver transplant recipients
Authors: Egawa H , Ozawa K , Takada Y , Teramukai S , Mori A , Ogawa K , Kaido T , Fujimoto Y , Kawaguchi Y , Hatano E , Sato H , Ono M , Takai K , Tanaka K , Uemoto S 
Published: May 2010

Summary
This study investigated how CD8+ T cell subsets respond to allo- and infectious immunity after living donor liver transplantation (LDLT). Early alloimmunity: 56 recipients were classified into three types according to the post-transplant course; type I demonstrated uneventful post-transplant course, type II developed severe sepsis leading to multiple organ dysfunction syndrome or retransplantation and type III with acute rejection. In 23 type I recipients, the interleukin (IL)-12 receptor beta-1 (Rβ1)+ cells of central memory T cells (Il-12Rβ1+ TCM) were increased above the pretransplant level. In 16 type II recipients, IL-12Rβ1+ TCM was decreased markedly below the pretransplant level on postoperative day (POD) 5. In 17 type III recipients, IL-12Rβ1+ TCM was decreased for a more prolonged period until POD 10. Along with down-regulation of IL-12Rβ1+ TCM, the IL-12Rβ1+ cells of CCR7-negative subsets (CNS) as well as perforin, interferon (IFN)-γ and tumour necrosis factor (TNF)-α decreased gradually, resulting in the down-regulation of effectors and cytotoxicity. The down-regulation of IL-12Rβ1+ TCM was suggested to be due to the recruitment of alloantigen-primed T cells into the graft, and then their entry into the secondary lymphoid organ, resulting in graft destruction. Infectious immunity: immunocompetent memory T cells with the capacity to enhance effectors and cytotoxicity were generated in response to post-transplant infection along with both up-regulation of the IL-12Rβ1+ TCM and an increase in the CNS showing the highest level of IL-12Rβ1+ cells. In conclusion, this work demonstrated that the IL-12Rβ1+ cells of TCM and CNS are regulated in a tightly coupled manner and that expression levels of IL-12Rβ1+ TCM play a crucial role in controlling allo- and infectious immunity.
Inhibition of neutrophil-mediated production of reactive oxygen species (ROS) by endothelial cells is not impaired in anti-neutrophil cytoplasmic autoantibodies (ANCA)-associated vasculitis patients
Authors: Al Laham F , Kälsch A-I , Heinrich L , Birck R , Kallenberg C G M , Heeringa P , Yard B 
Published: May 2010

SummaryLeucocyte transendothelial migration is strictly regulated to prevent undesired inflammation and collateral damage of endothelial cells by activated neutrophils/monocytes. We hypothesized that in anti-neutrophil cytoplasmic autoantibodies (ANCA)-associated vasculitis (AAV) patients' dysregulation of this process might underlie vascular inflammation. Peripheral blood mononuclear cells (PBMC) and neutrophils from AAV patients (n = 12) and healthy controls (HC, n = 12) were isolated. The influence of human umbilical vein endothelial cells (HUVEC) on neutrophil/monocytes function was tested by N-formyl-methionyl-leucyl-phenyl-alanine (fMLP)- and phorbol 12-myristate 13-acetate (PMA)-mediated ROS production, degranulation and interleukin (IL)-8 production. In addition, the ability of lipopolysaccharide (LPS)-stimulated PBMC to produce tumour necrosis factor (TNF)-α in the presence or absence of HUVEC was tested. HUVEC inhibited ROS production dose-dependently by fMLP-stimulated neutrophils but did not influence degranulation. No differences between neutrophils from HC and AAV were found. However, in only one active patient was degranulation inhibited significantly by HUVEC only before cyclophosphamide treatment, but not 6 weeks later. Co-cultures of HUVEC with LPS-stimulated neutrophils/monocytes increased IL-8 production while TNF-α production was inhibited significantly. There was no apparent difference between AAV patients and HC in this respect. Our findings demonstrate that HUVEC are able to inhibit ROS and modulate cytokine production upon stimulation of neutrophils or monocytes. Our data do not support the hypothesis that endothelial cells inhibit ROS production of neutrophils from AAV patients inadequately. Impaired neutrophil degranulation may exist in active patients, but this finding needs to be confirmed.
Survey of medical training in cytopathology carried out by the journal Cytopathology
Authors: Anshu  , Herbert A. , Cochand‐Priollet B. , Cross P. , Desai M. , Dina R. , Duskova J. , Evered A. , Farnsworth A. , Gray W. , Gupta S. S. , Kapila K. , Kardum‐Skelin I. , Kloboves‐Prevodnik V. , Kobayashi T. K. , Koutselini H. , Olszewski W. , Onal B. , Pitman M. B. , Marinšek Ž. , Sauer T. , Schenck U. , Schmitt F. , Shabalova I. , Smith J. H. F. , Tani E. , Vass L. , Vielh P. , Wiener H. 
Published: May 2010

Anshu, A. Herbert, B. Cochand‐Priollet, P. Cross, M. Desai, R. Dina, J. Duskova, A. Evered, A. Farnsworth, W. Gray, S. S. Gupta, K. Kapila, I. Kardum‐Skelin, V. Kloboves‐Prevodnik, T. K. Kobayashi, H. Koutselini, W. Olszewski, B. Onal, M. B. Pitman, Ž. Marinšek, T. Sauer, U. Schenck, F. Schmitt, I. Shabalova, J. H. F. Smith, E. Tani, L. Vass, P. Vielh and H. Wiener Survey of medical training in cytopathology carried out by the journal CytopathologyThis report of the Editorial Advisory Board of Cytopathology gives the results of a survey of medical practitioners in cytopathology, which aimed to find out their views on the current situation in undergraduate and postgraduate training in their institutions and countries. The results show that training in cytopathology and histopathology are largely carried out at postgraduate level and tend to be organized nationally rather than locally. Histopathology was regarded as essential for training in cytopathology by 89.5% of respondents and was mandatory according to 83.1%. Mandatory cytopathology sections of histopathology were reported by 67.3% and specific examinations in cytopathology by 55.4%. The main deficiencies in training were due to its variability; there were insufficient numbers of pathologists interested in cytology and a consequent lack of training to a high level of competence. Pathologists without specific training in cytopathology signed out cytology reports according to 54.7% of responses, more often in centres where training was 3–6 months or less duration. Although 92.2% of respondents thought that specialist cytology should not be reported by pathologists without experience in general cytopathology, that practice was reported by 30.9%, more often in centres with small workloads. The survey report recommends that 6–12 months should be dedicated to cytopathology during histopathology training, with optional additional training for those wanting to carry out independent practice in cytopathology. Formal accreditation should be mandatory for independent practice in cytopathology. When necessary, temporary placements to centres of good practice should be available for trainees intending to practise independently in cytopathology. There should be adequate numbers of pathologists trained in cytopathology to a high level of competence; some of their time could be released by training cytotechnologists and trainee pathologists to prescreen cytology slides and assess adequacy of fine‐needle aspiration samples when immediate diagnosis was not required. The survey demonstrated a clear need for European and international guidelines for training in cytopathology.
Differentiation of leaf water flux and drought tolerance traits in hemiepiphytic and non‐hemiepiphytic Ficus tree species
Authors: Hao Guang‐You , Sack Lawren , Wang Ai‐Ying , Cao Kun‐Fang , Goldstein Guillermo 
Published: May 2010

Summary 1. Leaf structural and physiological traits are associated with growth form and habitat, but little is known of the specific traits associated with hemiepiphytes, which are an important component of many tropical forests. Given their life history that includes a drought prone epiphytic stage, hemiepiphytes should be expected to have more drought tolerance‐related traits than co‐occurring terrestrial species. 2. The genus Ficus includes woody hemiepiphytes distributed in tropical areas throughout the world. Traits related to the flux of water through the leaf and to drought adaptations were studied in five hemiephiphytic (H) and five non‐hemiepiphytic (NH) Ficus tree species grown in a common garden to determine genetically based differences. 3. Leaves of H and NH species differed substantially in structure and physiology; on average, H species had smaller leaves with higher leaf mass per unit area, thicker epidermis, smaller vessel lumen diameters in petioles and lower petiole hydraulic conductivity. Leaf traits also indicated stronger drought tolerance in H species, including lower epidermal conductance and turgor loss point and earlier stomatal closure with desiccation than NH species. Across H and NH species, traits related to water flux capacity were negatively correlated with traits related to drought tolerance. 4. The divergences in hydraulics and water relations between growth forms for these closely related species reflected specialization according to contrasting habitat and life form. Conservative water use and increased ability of leaves to persist under severe drought would provide an advantage for H species, especially during the epiphytic phase, while the higher potential water use of NH species would be associated with higher assimilation rates and competitiveness under high water supply. 5. The results indicate a trade‐off between leaf water flux capacity and leaf drought tolerance across these hemiephiphytic and non‐hemiepiphytic species. Species adaptation to habitats with contrasting demands on leaf function may lead to divergence along a leaf water‐flux‐droughttolerance spectrum.
Multi‐tasking of helper T cells
Authors: Wan Yisong Y. 
Published: May 2010

SummaryCD4 T helper cells (Th) are critical in combating pathogens and maintaining immune homeostasis. Since the establishment of the Th1–Th2 paradigm in the 1980s, many types of specialized Th cells, including Th1, Th2, Th17, Th9, follicular helper T and regulatory T, have been identified. We have become accustomed to the idea that different Th cells are ‘committed’ to their paths but recent emerging evidence suggests that under certain conditions, seemingly committed Th cells possess plasticity and may convert into other types of effector cells. In this review, we will first introduce the major sub‐types of Th cells that are involved in immune regulation. Then, we will describe in detail the inter‐convertibility of Th cells among different sub‐types under in vitro and in vivo conditions. Finally, we will discuss our current understanding of the underlying mechanisms on how a particular type of Th cells may convert into other types of Th cells.