bluuebunny/crossref_metadata_2025_split huggingface dataset:
General coupling extended multiscale FEM for elasto‐plastic consolidation analysis of heterogeneous saturated porous media
Authors: Zhang Hongwu , Lu Mengkai , Zheng Yonggang , Zhang Sheng 
Published: May 2014

SUMMARYThis paper presents a general coupling extended multiscale FEM (GCEMs) for solving the coupling problem of elasto‐plastic consolidation of heterogeneous saturated porous media. In the GCEMs, the numerical multiscale base functions for the solid skeleton and fluid phase of the coupling system are all constructed on the basis of the equivalent stiffness matrix of the unit cell, which not only contain the interaction between the solid and fluid phases but also consider the time effect. Furthermore, in order to improve the computational accuracy for two‐dimensional problems, a multi‐node coarse element strategy for the GCEMs is proposed, and a two‐scale iteration algorithm for the elasto‐plastic consolidation analysis is developed. Some one‐dimensional and two‐dimensional homogeneous and heterogeneous numerical examples are carried out to validate the proposed method through the comparison with the coupling multiscale FEM and standard FEM. Numerical results show that the newly developed GCEMs can almost preserve the same convergent property as the standard FEM and also possesses the advantages of high computational efficiency. In addition, the GCEMs can be easily applied to other coupling multifield and multiphase transient problems. Copyright © 2014 John Wiley & Sons, Ltd.
Image‐based simulation of urethral distensibility and flow resistance as a function of pelvic floor anatomy
Authors: Yao Franklin , Laudano Melissa A. , Seklehner Stephan , Chughtai Bilal , Lee Richard K. 
Published: May 2014

AbstractAimsThe goal of this study is to develop an image‐based model of urethral distention and resistance in women with and without SUI.MethodsA biomechanical vector force model was created to simulate the mechanical deformation of pelvic floor structures during cough and Valsalva in order to measure urethral distension and predict flow resistance patterns. Dynamic MRI images were used to create a spatial model to construct an accurate representation of tissue thickness and location, which was combined with tissue property values (MATLAB 2011a, MathWorks, Natick, MA). Spatial profiles were created to demonstrate the effects of hypermobility and tissue property variability on distensibility and flow resistance along the urethra. Sensitivity analyses were conducted to demonstrate the relationship between flow resistance and various tissue properties.ResultsThe average distension for incontinent cases (3.8 mm) was significantly greater than that of continent cases (2.6 mm) (t = 3.3083, df = 8, P < 0.01), corresponding to a 70% drop in average resistance to urine flow. Sensitivity analyses demonstrated that the stiffness and contractility of the vagina and urethra had the greatest effect on continence.ConclusionsWe present a novel, 2‐dimensional biomechanical model of female stress urinary incontinence (SUI) that relates the effects of various factors such as tissue elasticity, pelvic floor structure, and muscle activation. A better understanding of the pathophysiology underlying SUI has potential implications for the creation of novel targeted treatments. Neurourol. Urodynam. 34:???–???, 2015. © 2014 Wiley Periodicals, Inc.
Rapidly derived colorectal cancer cultures recapitulate parental cancer characteristics and enable personalized therapeutic assays
Authors: Ashley Neil , Jones Matthew , Ouaret Djamila , Wilding Jenny , Bodmer Walter F 
Published: May 2014

AbstractWe have developed a simple procedure for deriving pure cultures of growing cancer cells from colorectal cancers, including material refrigerated overnight, for pathological characterization and cytotoxicity assays. Forty‐six cancers were processed and cultures set up under varying culture conditions. Use of a Rho kinase (ROCK1) inhibitor markedly increased culture survival, resulting in 80% of samples growing in culture for at least 1 month and beyond. Overnight refrigeration of samples before culture initiation had little effect on success rates, paving the way for cultures to be established for samples collected over wide geographical areas, such as those for clinical trials. Primary cultures demonstrated good correlation for differentiation markers compared to parent cancers, and were highly dynamic in 3D culture. In Matrigel, many colonies formed central lumens, indicating the presence of stem‐like cells. Viable colonies in these cultures recapitulated the in vivo generation of carcinoembryonic antigen (CEA)‐positive necrotic/apoptotic debris, much of which was derived from abnormal vacuolated dynamic ‘bubble cells’ that have not previously been described. Although bubble cells morphologically resembled signet ring cells, a rare cancer subtype, immunostaining suggested that they were most likely derived from terminally differentiated enterocytes. Micro‐assays showed that drug toxicity could be measured in these cultures within hours and with sensitivity down to a few hundred cells. Primary cultures derived by our method provide valid in vitro avatars for studying the pathology of cancers in vitro and are amenable to pre‐clinical drug testing, paving the way for personalized cancer treatment. Copyright © 2014 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Phase transitions in lipid vesicles detected by a complementary set of methods: heat‐transfer measurements, adiabatic scanning calorimetry, and dissipation‐mode quartz crystal microbalance
Authors: Losada‐Pérez P. , Jiménez‐Monroy K. L. , van Grinsven B. , Leys J. , Janssens S. D. , Peeters M. , Glorieux C. , Thoen J. , Haenen K. , De Ceuninck W. , Wagner P. 
Published: May 2014

We report on the use of the heat transfer method, a novel surface‐sensitive technique based on heat transfer through solid–liquid interfaces, to detect phase transitions of model lipid membranes. We selected the lipid DPPC because of its rich phase behavior in an experimentally accessible temperature range. The vesicles were adsorbed on nanocrystalline diamond films, known as a versatile platform material for biosensing with outstanding heat‐conduction properties. Complementary Peltier‐element‐based adiabatic scanning calorimetry (pASC) and quartz crystal microbalance with dissipation monitoring (QCM‐D) measurements were carried out to monitor the phase transitions in multilamellar and small unilamellar vesicles, respectively. The heat‐transfer measurements revealed reversible jumps upon heating and cooling in the thermal resistance in the vicinity of the expected transition temperature and they agree qualitatively with molecular simulations of the thermal conductivity across a lipid bilayer. The results show the capability of the heat transfer method to detect the main phase transition in DPPC, opening new perspectives for the study of more complex lipid systems and different solid platforms. This work confirms QCM‐D as a useful tool for the assessment of the structural changes upon the phase conversion and shows the capability of pASC to provide high‐resolution thermodynamic information on biophysical systems.Temperature profile of the heat transfer resistance Rth during the main phase transition of a DPPC supported vesicle layer adsorbed on a hydrogen‐terminated nanocrystalline diamond substrate. The arrows indicate the sense of the run: heating (red solid line) and cooling (blue solid line).
Temporal Variations in Dissolved Oxygen Concentrations Observed in a Shallow Floodplain Aquifer
Authors: Schilling K. E. , Jacobson P. J. 
Published: May 2014

AbstractDissolved oxygen (DO) concentrations play an important role in many groundwater biogeochemial processes, yet assessments of temporal variations are lacking. In this study, we examined daily DO concentrations using a continuously‐reading optical DO probe in a shallow floodplain setting in Iowa to (i) quantify fluctuations across two growing seasons; (ii) examine hydrologic controls on DO values; and (iii) model daily DO concentrations using easily measured variables. DO concentrations exhibited both rapid and long‐term changes in concentrations over time, rapidly increasing and decreasing more than 1 mg/l in response to precipitation recharge and stream stage increase over the span of several hours and days. On 40% of the monitoring days in this study, DO concentrations increased, on average, 0.2–0.4 mg/l from one day to the next. DO concentrations decreased approximately 5–6 mg/l from spring through late summer and fall, likely owing to microbial and root respiration. Daily DO concentrations were successfully modelled using a combination of hydrologic (groundwater level and river stage) and temperature variables (r2 > 0.7). Improved understanding of temporal controls on groundwater DO patterns is needed to help clarify the dynamics of many biogeochemical processes. Copyright © 2014 John Wiley & Sons, Ltd.
Exploring and inferring user–user pseudo‐friendship for sentiment analysis with heterogeneous networks
Authors: Deng Hongbo , Han Jiawei , Li Hao , Ji Heng , Wang Hongning , Lu Yue 
Published: May 2014

AbstractWith the development of social media and social networks, user‐generated content, such as forums, blogs and comments, are not only getting richer, but also ubiquitously interconnected with many other objects and entities, forming a heterogeneous information network between them. Sentiment analysis on such kinds of data can no longer ignore the information network, since it carries a lot of rich and valuable information, explicitly or implicitly, where some of them can be observed while others are not. However, most existing methods may heavily rely on the observed user–user friendship or similarity between objects, and can only handle a subgraph associated with a single topic. None of them takes into account the hidden and implicit dissimilarity, opposite opinions, and foe relationship. In this paper, we propose a novel information network‐based framework which can infer hidden similarity and dissimilarity between users by exploring similar and opposite opinions, so as to improve post‐level and user‐level sentiment classification at the same time. More specifically, we develop a new meta path‐based measure for inferring pseudo‐friendship as well as dissimilarity between users, and propose a semi‐supervised refining model by encoding similarity and dissimilarity from both user‐level and post‐level relations. We extensively evaluate the proposed approach and compare with several state‐of‐the‐art techniques on two real‐world forum datasets. Experimental results show that our proposed model with 10.5% labeled samples can achieve better performance than a traditional supervised model trained on 61.7% data samples.
Learning about application software by studying processes
Authors: Osterweil Leon J. 
Published: May 2014

ABSTRACTIn earlier work, it has been suggested that processes and applications seem to share many important characteristics and seem to be amenable to similar approaches of modeling, definition, and analysis. In most of this previous work, approaches and technologies for developing applications have been applied to the development of processes, largely with positive results. This paper suggests the opposite, namely that approaches and technologies for developing processes seem likewise to be applicable to developing applications. As an example, this paper notes that resource specification, allocation, and management are central issues in the development of many processes, and suggests that although these capabilities seem to be important for growing classes of application software, the ability to support them seems curiously neglected. The paper also notes that management of rework is a central issue of virtually all creative activities. This is evidenced by the observation that facilities for supporting rework are prominent features in so many creative domains. Accordingly, the paper suggests an analogous need for facilities for supporting rework in application software as well, especially in application software aimed at supporting human creativity. The paper concludes by noting that both application and process software technologies grow through consideration of the relevance of technologies developed for one to the other. This in turn should lead to a clearer understanding of the essence of what they have in common, leading to conjectures about the nature of a more abstract class of entities, that we refer to simply as software. Copyright © 2014 John Wiley & Sons, Ltd.
Concerned with the unprivileged: user programs in kernel refinement
Authors: Daum Matthias , Billing Nelson , Klein Gerwin 
Published: May 2014

Abstract
It is a great verification challenge to prove properties of complete computer systems on the source code level. The L4.verified project achieved a major step towards this goal by mechanising a proof of functional correctness of the seL4 kernel. They expressed correctness in terms of data refinement with a coarse-grained specification of the kernel’s execution environment. In this paper, we strengthen the original correctness theorem in two ways. First, we convert the previous abstraction relations into projection functions from concrete to abstract states. Second, we revisit the specification of the kernel’s execution environment: we introduce the notion of virtual memory based on the kernel data structures, we distinguish individual user programs that run on top of the kernel and we restrict the memory access of each of these programs to its virtual memory. Through our work, properties like the separation of user programs gain meaning. This paves the way for proving security properties like non-interference of user programs. Furthermore, our extension of L4.verified’s proof facilitates the verification of properties about complete software systems based on the seL4 kernel. Besides the seL4-specific results, we report on our work from an engineering perspective to exemplify general challenges that similar projects are likely to encounter. Moreover, we point out the advantages of using projection functions in L4.verified’s verification approach and for stepwise refinement in general.
Assessment of low-dose cisplatin as a model of nausea and emesis in beagle dogs, potential for repeated administration
Authors: Kenward Hannah , Pelligand Ludovic , Elliott Jonathan 
Published: May 2014

AbstractCisplatin is a highly emetogenic cancer chemotherapy agent, which is often used to induce nausea and emesis in animal models. The cytotoxic properties of cisplatin also cause adverse events that negatively impact on animal welfare preventing repeated administration of cisplatin. In this study, we assessed whether a low (subclinical) dose of cisplatin could be utilized as a model of nausea and emesis in the dog while decreasing the severity of adverse events to allow repeated administration. The emetic, nausea-like behavior and potential biomarker response to both the clinical dose (70 mg/m2) and low dose (15 mg/m2) of cisplatin was assessed. Plasma creatinine concentrations and granulocyte counts were used to assess adverse effects on the kidneys and bone marrow, respectively. Nausea-like behavior and emesis was induced by both doses of cisplatin, but the latency to onset was greater in the low-dose group. No significant change in plasma creatinine was detected for either dose groups. Granulocytes were significantly reduced compared with baseline (P = 0.000) following the clinical, but not the low-dose cisplatin group. Tolerability of repeated administration was assessed with 4 administrations of an 18 mg/m2dose cisplatin. Plasma creatinine did not change significantly. Cumulative effects on the granulocytes occurred, they were significantly decreased (P = 0.03) from baseline at 3 weeks following cisplatin for the 4th administration only. Our results suggest that subclinical doses (15 and 18 mg/m2) of cisplatin induce nausea-like behavior and emesis but have reduced adverse effects compared with the clinical dose allowing for repeated administration in crossover studies.
Prediction of Permanent Hypoparathyroidism after Total Thyroidectomy
Authors: Almquist M. , Hallgrimsson P. , Nordenström E. , Bergenfelz A. 
Published: May 2014

AbstractBackground
Hypoparathyroidism is a common complication with thyroid surgery. The ability to predict a high risk of permanent hypoparathyroidism is important for individual prognosis and follow‐up.MethodsPermanent hypoparathyroidism, defined as continuing need for vitamin D medication at 1‐year post‐operatively, was investigated in patients after total thyroidectomy. Blood levels of calcium and parathyroid hormone (PTH) were measured intra‐operatively, the day after surgery and at 1 month post‐operatively. Logistic regression analysis was performed to investigate the risk of vitamin D treatment at last follow‐up, calculated as odds ratios (ORs) with 95 % confidence intervals (CIs). Patients were followed until cessation of vitamin D and/or calcium medication, until death, loss to follow‐up, or end of follow‐up, whichever came first.ResultsA total of 519 patients were included. The median (range) follow‐up in patients unable to cease vitamin D was 2.7 (1.2–10.3) years. The rate of permanent hypoparathyroidism was 10/519, 1.9 %. Parathyroid auto‐transplantation was performed in 90/519 (17.3 %) patients. None of these developed permanent hypoparathyroidism, nor did any patient with normal PTH day 1 (>1.6 pmol/l or 15 pg/ml). The adjusted risk (OR, 95 % CI) for permanent hypoparathyroidism for log PTH on day 1 was 0.25 (0.13–0.50). In patients not auto‐transplanted and with unmeasurable PTH day 1 (<0.7 pmol/l or 6.6 pg/ml), 8/42 (19.2 %) developed permanent hypoparathyroidism.ConclusionsAuto‐transplantation protects against permanent hypoparathyroidism, whereas low PTH day 1 is associated with high risk.
Synergistic effects of primates and dung beetles on soil seed accumulation in snow regions
Authors: Enari Hiroto , Sakamaki‐Enari Haruka 
Published: May 2014

AbstractThis study aimed to reveal the soil seed accumulation processes for endozoochorous plants in the heavy‐snowfall forests of Japan, where seed dispersal agents are few when compared to tropical forests. We assessed (1) primary seed dispersal by Japanese macaques (Macaca fuscata) by identifying dispersed seeds found in their feces, and (2) secondary seed dispersal by dung beetles by using beads (as seeds mimics) of different sizes, to quantify the frequency of seed burial and burial depths. We studied this diplochorous system in different forest types (undisturbed beech forest, conifer plantation, and secondary beech‐oak forest) and during the spring and summer seasons. The key findings were as follows: (1) macaques dispersed the seeds of 11 and 14 plant species during spring and summer, respectively; (2) seeds dispersed by macaques in the spring were smaller and twice as abundant than those dispersed in the summer; (3) although no differences were observed in the amount of beads buried by beetles between seasons, all bead sizes tended to be buried in deeper soil layers in the spring than in the summer; and (4) the seed supply to the soil in undisturbed beech forest and conifer plantation was greater than the one in secondary beech‐oak forest. Similar to what has been observed in tropical forests, seeds defecated by frugivorous mammals can be successfully incorporated into the underground soil seed bank through a diplochorous macaque‐beetle system in temperate forests of deep snow regions.
Practical Aspects of Risk Assessment in Gastrointestinal Stromal Tumors
Authors: Jones R. L. 
Published: May 2014

Abstract
Introduction
Gastrointestinal stromal tumors (GISTs) are mesenchymal tumors of the gastrointestinal tract, which are characterized in the majority of cases by activating mutations in KIT and platelet-derived growth factor receptor alpha (PDGFRA). The introduction of tyrosine kinase inhibitors has revolutionized the management of patients with metastatic GIST. However, complete surgical resection remains the mainstay of management for those with localized disease. Recently, three large trials have confirmed the benefit of adjuvant imatinib therapy in patients who were at high risk of recurrence following complete resection. In this setting, it is critical that oncologists understand the various GIST risk assessment criteria and be able to apply these methods to accurately assess the risk of recurrence and the need for adjuvant imatinib therapy.

Purpose
The aim of this review is to outline the risk stratification systems currently available to oncologists who are treating patients with GIST, so they can be optimally applied for clinical decision-making.
A conceptual framework for research on subjective cognitive decline in preclinical Alzheimer's disease
Authors: Jessen Frank , Amariglio Rebecca E. , van Boxtel Martin , Breteler Monique , Ceccaldi Mathieu , Chételat Gaël , Dubois Bruno , Dufouil Carole , Ellis Kathryn A. , van der Flier Wiesje M. , Glodzik Lidia , van Harten Argonde C. , de Leon Mony J. , McHugh Pauline , Mielke Michelle M. , Molinuevo Jose Luis , Mosconi Lisa , Osorio Ricardo S. , Perrotin Audrey , Petersen Ronald C. , Rabin Laura A. , Rami Lorena , Reisberg Barry , Rentz Dorene M. , Sachdev Perminder S. , de la Sayette Vincent , Saykin Andrew J. , Scheltens Philip , Shulman Melanie B. , Slavin Melissa J. , Sperling Reisa A. , Stewart Robert , Uspenskaya Olga , Vellas Bruno , Visser Pieter Jelle , Wagner Michael ,   Subjective Cognitive Decline Initiative (SCD‐I) Working Group
Published: May 2014

AbstractThere is increasing evidence that subjective cognitive decline (SCD) in individuals with unimpaired performance on cognitive tests may represent the first symptomatic manifestation of Alzheimer's disease (AD). The research on SCD in early AD, however, is limited by the absence of common standards. The working group of the Subjective Cognitive Decline Initiative (SCD‐I) addressed this deficiency by reaching consensus on terminology and on a conceptual framework for research on SCD in AD. In this publication, research criteria for SCD in pre‐mild cognitive impairment (MCI) are presented. In addition, a list of core features proposed for reporting in SCD studies is provided, which will enable comparability of research across different settings. Finally, a set of features is presented, which in accordance with current knowledge, increases the likelihood of the presence of preclinical AD in individuals with SCD. This list is referred to as SCD plus.
Clinical utility of cerebrospinal fluid biomarkers in the diagnosis of early Alzheimer's disease
Authors: Blennow Kaj , Dubois Bruno , Fagan Anne M. , Lewczuk Piotr , de Leon Mony J. , Hampel Harald 
Published: May 2014

AbstractSeveral potential disease‐modifying drugs for Alzheimer's disease (AD) have failed to show any effect on disease progression in clinical trials, conceivably because the AD subjects are already too advanced to derive clinical benefit from treatment and because diagnosis based on clinical criteria alone introduces a high misdiagnosis rate. Thus, well‐validated biomarkers for early detection and accurate diagnosis are crucial. Low cerebrospinal fluid (CSF) concentrations of the amyloid‐β (Aβ1‐42) peptide, in combination with high total tau and phosphorylated tau, are sensitive and specific biomarkers highly predictive of progression to AD dementia in patients with mild cognitive impairment. However, interlaboratory variations in the results seen with currently available immunoassays are of concern. Recent worldwide standardization efforts and quality control programs include standard operating procedures for both preanalytical (e.g., lumbar puncture and sample handling) and analytical (e.g., preparation of calibration curve) procedures. Efforts are also ongoing to develop highly reproducible assays on fully automated instruments. These global standardization and harmonization measures will provide the basis for the generalized international application of CSF biomarkers for both clinical trials and routine clinical diagnosis of AD.