bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fatigue in relatives of palliative patients
Authors: Carlsson Maria E. 
Published: June 2009

ABSTRACTObjectives:The relatives’ burdens in palliative care are considerable and may cause fatigue. The overall aim of this study was to gain a greater understanding of fatigue in relatives of patients cared for in palliative care settings.Methods:This study has a descriptive, comparative, and cross-sectional design. The sample consisted of relatives of all patients cared for in palliative care settings in Uppsala County during a specific day. Relatives completed a questionnaire consisting of the Multidimensional Fatique Inventory (MFI-20) and questions from the Karolinska Sleepiness Scale (KSS) and Karolinska Sleep questionnaire (KSQ).Results:Relatives (n = 56) scored high on every dimension on the MFI-20 scale. Two significant negative correlations were found to exist between age and fatigue, with younger relatives reporting more mental fatigue (p < .01) and more reduced activity (p < .01) than older relatives. Relatives of patients in institutional care had higher values concerning mental fatigue (p < .01) and reduced motivation (p < .05). Relatives of mostly bedridden patients were significantly more tired but did not have significantly less motivation than relatives of mostly ambulatory patients.Significance of results:The findings imply that fatigue is highly prevalent in relatives of patients in palliative care. The sample in this study scored higher in comparison with norm values and also in comparison with relatives of patients with end-stage renal disease. Their scores were similar to those of cancer patients undergoing radiotherapy.
Using the differential from complete blood counts as a biomarker of fatigue in advanced non-small-cell lung cancer: An exploratory analysis
Authors: Paddison Johanna S. , Temel Jennifer S. , Fricchione Gregory L. , Pirl William F. 
Published: June 2009

ABSTRACTObjective:Fatigue is currently recognized as an undertreated symptom in cancer. To date the association between fatigue and inflammatory activation has not been examined in patients with advanced cancer. Our exploratory investigation considered whether variations in routinely available hematological parameters relate to the severity of fatigue reports.Methods:Fatigue, white blood cell differential, and hemoglobin concentration were assessed in 44 Stage IIIb and IV non-small-cell lung cancer (NSCLC) patients. Days of survival and the relative timing of treatment discontinuation were also recorded. Relationships between fatigue intensity and length of survival and between fatigue and hematological variables were examined using binomial and linear regressions respectively.Results:When we controlled for effects related to age, gender, and time until treatment termination, more intense fatigue was associated with shorter survival (β = −.34, p = .03). Lower hemoglobin concentrations were associated with more intense fatigue (β = −.36, p = .04). When we controlled for the effect attributable to hemoglobin, higher neutrophil (β = .43, p = .01) and monocyte (β = .31, p = .05) concentrations were associated with reports of more severe fatigue.Significance of results:This exploratory study provides empiric data showing that the severity of fatigue reported by advanced-stage NSCLC patients is significantly associated with length of survival. Consistent with existing data, linear regression identified a negative association between fatigue intensity and hemoglobin concentration. When we controlled for this effect, further linear regressions identified significant relationships between fatigue and blood concentrations of neutrophils and monocytes. Further, the magnitude of relationship between myeloid cell concentrations and fatigue was similar to the effect size identified for the relationship between hemoglobin and fatigue. Thus, the indirect measure of inflammatory state provided by routinely assessed myeloid cell counts appears to play as strong a role as the established variable, hemoglobin, in accounting for the fatigue reported by this sample of advanced-stage lung cancer patients.
Effect of music therapy on oncologic staff bystanders: A substantive grounded theory
Authors: O'Callaghan Clare , Magill Lucanne 
Published: June 2009

ABSTRACTObjective:Oncologic work can be satisfying but also stressful, as staff support patients and families through harsh treatment effects, uncertain illness trajectories, and occasional death. Although formal support programs are available, no research on the effects of staff witnessing patients' supportive therapies exists. This research examines staff responses to witnessing patient-focused music therapy (MT) programs in two comprehensive cancer centers.Method:In Study 1, staff were invited to anonymously complete an open-ended questionnaire asking about the relevance of a music therapy program for patients and visitors (what it does; whether it helps). In Study 2, staff were theoretically sampled and interviewed regarding the personal effects of witnessing patient-centered music therapy. Data from each study were comparatively analyzed according to grounded theory procedures. Positive and negative cases were evident and data saturation arguably achieved.Results:In Study 1, 38 staff unexpectedly described personally helpful emotional, cognitive, and team effects and consequent improved patient care. In Study 2, 62 staff described 197 multiple personal benefits and elicited patient care improvements. Respondents were mostly nursing (57) and medical (13) staff. Only three intrusive effects were reported: audibility, initial suspicion, and relaxation causing slowing of work pace. A substantive grounded theory emerged applicable to the two cancer centers: Staff witnessing MT can experience personally helpful emotions, moods, self-awarenesses, and teamwork and thus perceive improved patient care. Intrusive effects are uncommon. Music therapy's benefits for staff are attributed to the presence of live music, the human presence of the music therapist, and the observed positive effects in patients and families.Significance of results:Patient-centered oncologic music therapy in two cancer centers is an incidental supportive care modality for staff, which can reduce their stress and improve work environments and perceived patient care. Further investigation of the incidental benefits for oncologic staff witnessing patient-centered MT, through interpretive and positivist measures, is warranted.
Cancer patients' reluctance to discuss psychological distress with their physicians was not associated with underrecognition of depression by physicians: A preliminary study
Authors: Okuyama Toru , Endo Chiharu , Seto Takashi , Kato Masashi , Seki Nobuhiko , Akechi Tatsuo , Furukawa Toshiaki A. , Eguchi Kenji , Hosaka Takashi 
Published: June 2009

ABSTRACTObjective:To investigate the association between cancer patients' reluctance for emotional disclosure to their physician and underrecognition of depression by physicians.Methods:Randomly selected ambulatory patients with lung cancer were evaluated by the Hospital Depression and Anxiety Scale (HADS), and those with scores over the validated cutoff value for adjustment disorder or major depressive disorder were included in this analysis. The data set included the responses to the 13-item questionnaire to assess four possible concerns of patients in relation to emotional disclosure to the treating physician (“no perceived need to disclose emotions,” “fear of the negative impact of emotional disclosure,” “negative attitude toward emotional disclosure,” “hesitation to disturb the physician with emotional disclosure”). The attending physicians rated the severity of depression in each patient using 3-point Likert scales (0 [absent] to 2 [clinical]). Depression was considered to be underrecognized when the patients had a HADS score above the cutoff value, but in whom the depression rating by the attending physician was 0.Results:The HADS score was over the cutoff value in the 60 patients. The mean age was 65.1 ± 10.0, and 82% had advanced cancer (Stage IIIb or IV or recurrence). Depression was underrecognized in 44 (73%) patients. None of the four factors related to reluctance for emotional disclosure was associated with the underrecognition of depression by the physicians. None of the demographic or cancer–related variables were associated with depression underrecognition by physicians.Significance of results:The results did not support the assumption that patients' reluctance for emotional disclosure is associated with the underrecognition of depression by physicians.
Staff grief and support systems for Japanese health care professionals working in palliative care
Authors: Shimoinaba Kaori , O'Connor Margaret , Lee Susan , Greaves Judi 
Published: June 2009

ABSTRACTObjective:This article is a literature report on grief issues for health care professionals, undertaken to identify Japanese nurses' grief experience when they work in palliative care units. Health care professionals' grief experience and its impact have not been well understood or identified as a significant issue in Japan.Methods:Published articles relating to this study were searched using electronic catalogues such as CINAHL and PsycINFO, books, and research publications. Key words used for the search were “grief,” “palliative care,” “nurse,” “staff support,” and “Japan.” Both English and Japanese were used for the literature search in order to collect information regarding nurses' grief and support systems in Japan and elsewhere. The literature search covered the period 1990–2006 inclusive.Results:This article explores these issues in the literature as preparation for establishing a study that will particularly look at the influence of nurses' grief on the quality of care provided.Significance of results:Consideration of Japanese culture as it relates to death and dying and to nursing culture is a significant part of this work.
When cancerophobia and denial lead to death
Authors: Reich Michel , Gaudron Cecile , Penel Nicolas 
Published: June 2009

ABSTRACTObjective:The belief that cancer inevitably leads to a dreadful and painful death is widespread. This may contribute to society's cancerophobia and denial with subsequent frequent delays in seeking medical attention and treatment for suspected cancer. Cancerophobia is an active behavior of fear of cancer that can lead to repeated medical examination without giving full reassurance to the patient. Denial is a mechanism of defense that usually helps the patient to cope with painful, threatening, overwhelming, or awkward thoughts. When it turns out to be ineffective and pathological, it can cause either delay or avoidance in seeking treatment for symptoms relevant for a true malignancy and will lead inexorably to death if not cured.Method:To illustrate this, we report the case of a 62-year-old woman who died of massive concealed ovarian cancer, straightaway at a palliative stage, who always had a persistent denial of her medical condition and a past history of cancerophobia.Results:With this case report, we would like to point out that supportive or palliative care staff should pay attention to this lethal behavior.Significance of results:Some brief recommendations to deal with this specific problematic are outlined.
Specific rhizosphere bacterial and fungal groups respond differently to elevated atmospheric CO2
Authors: Drigo Barbara , van Veen Johannes A , Kowalchuk George A 
Published: June 2009

Abstract
Soil community responses to increased atmospheric CO2 concentrations are expected to occur mostly through interactions with changing vegetation patterns and plant physiology. To gain insight into the effects of elevated atmospheric CO2 on the composition and functioning of microbial communities in the rhizosphere, Carex arenaria (a non-mycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown under defined atmospheric conditions with either ambient (350 p.p.m.) or elevated (700 p.p.m.) CO2 concentrations. PCR-DGGE (PCR-denaturing gradient gel electrophoresis) and quantitative-PCR were carried out to analyze, respectively, the structure and abundance of the communities of actinomycetes, Fusarium spp., Trichoderma spp., Pseudomonas spp., Burkholderia spp. and Bacillus spp. Responses of specific functional groups, such as phloroglucinol, phenazine and pyrrolnitrin producers, were also examined by quantitative–PCR, and HPLC (high performance liquid chromatography) was employed to assess changes in exuded sugars in the rhizosphere. Multivariate analysis of group-specific community profiles showed disparate responses to elevated CO2 for the different bacterial and fungal groups examined, and these responses were dependent on plant type and soil nutrient availability. Within the bacterial community, the genera Burkholderia and Pseudomonas, typically known as successful rhizosphere colonizers, were significantly influenced by elevated CO2, whereas the genus Bacillus and actinomycetes, typically more dominant in bulk soil, were not. Total sugar concentrations in the rhizosphere also increased in both plants in response to elevated CO2. The abundances of phloroglucinol-, phenazine- and pyrrolnitrin-producing bacterial communities were also influenced by elevated CO2, as was the abundance of the fungal genera Fusarium and Trichoderma.
Range-based techniques for discovering optimality and analyzing scaling relationships in neuromechanical systems
Authors: Alicea Bradly 
Published: June 2009

AbstractIn this paper, a method for decoupling the neuromuscular function of a set of limbs from the role morphology plays in regulating the performance of an activity is introduced. This method is based on two previous methods: the rescaled range analysis specific to time series data, and the use of scaling laws. A review of the literature suggests that limb geometry can either facilitate or constrain performance as measured experimentally. Whether limb geometry is facilitatory or acts as a constraint depends on the size differential between arm morphology and the underlying muscle. "Changes in size and shape" are theoretically extrapolations of morphological geometry to other members of a population or species, to other species, or to technological manipulations of an individual via prosthetic devices. Three datasets are analyzed using the range-based method and a Monte-Carlo simulation, and are used to test the various ways of executing this analysis. It was found that when performance is kept stable but limb size and shape is scaled by a factor of .25, the greatest gain in performance results. It was also found that introducing force-based perturbations results in 'shifts' in the body geometry/performance relationship. While results such as this could be interpreted as a statistical artifact, the non-linear rise within a measurement class and linear decrease between measurement classes suggests an effect of scale in the optimality of this relationship. Overall, range-based techniques allow for the simulation and modeling of myriad changes in phenotype that result from biological and technological manipulation.
MEMS-based microspectrometer technologies for NIR and MIR wavelengths
Authors: Schuler Leo P , Milne Jason S , Dell John M , Faraone Lorenzo 
Published: June 2009

Commercially manufactured near-infrared (NIR) instruments became available about 50 years ago. While they have been designed for laboratory use in a controlled environment and boast high performance, they are generally bulky, fragile and maintenance intensive, and therefore expensive to purchase and maintain.Micromachining is a powerful technique to fabricate micromechanical parts such as integrated circuits. It was perfected in the 1980s and led to the invention of micro electro mechanical systems (MEMSs). The three characteristic features of MEMS fabrication technologies are miniaturization, multiplicity and microelectronics. Combined, these features allow the batch production of compact and rugged devices with integrated intelligence. In order to build more compact, more rugged and less expensive NIR instruments, MEMS technology has been successfully integrated into a range of new devices.In the first part of this paper we discuss the UWA MEMS-based Fabry–Pérot spectrometer, its design and issues to be solved. MEMS-based Fabry–Pérot filters primarily isolate certain wavelengths by sweeping across an incident spectrum and the resulting monochromatic signal is detected by a broadband detector. In the second part, we discuss other microspectrometers including other Fabry–Pérot spectrometer designs, time multiplexing devices and mixed time/space multiplexing devices.
An investigation into the population abundance distribution of mRNAs, proteins, and metabolites in biological systems
Authors: Lu Chuan , King Ross D. 
Published: June 2009

Abstract
Motivation: Distribution analysis is one of the most basic forms of statistical analysis. Thanks to improved analytical methods, accurate and extensive quantitative measurements can now be made of the mRNA, protein and metabolite from biological systems. Here, we report a large-scale analysis of the population abundance distributions of the transcriptomes, proteomes and metabolomes from varied biological systems.
Results: We compared the observed empirical distributions with a number of distributions: power law, lognormal, loglogistic, loggamma, right Pareto-lognormal (PLN) and double PLN (dPLN). The best-fit for mRNA, protein and metabolite population abundance distributions was found to be the dPLN. This distribution behaves like a lognormal distribution around the centre, and like a power law distribution in the tails. To better understand the cause of this observed distribution, we explored a simple stochastic model based on geometric Brownian motion. The distribution indicates that multiplicative effects are causally dominant in biological systems. We speculate that these effects arise from chemical reactions: the central-limit theorem then explains the central lognormal, and a number of possible mechanisms could explain the long tails: positive feedback, network topology, etc. Many of the components in the central lognormal parts of the empirical distributions are unidentified and/or have unknown function. This indicates that much more biology awaits discovery.
Contact: rdk@aber.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Modeling multi-cellular behavior in epidermal tissue homeostasis via finite state machines in multi-agent systems
Authors: Sütterlin Thomas , Huber Simone , Dickhaus Hartmut , Grabe Niels 
Published: June 2009

Abstract
Motivation: For the efficient application of multi-agent systems to spatial and functional modeling of tissues flexible and intuitive modeling tools are needed, which allow the graphical specification of cellular behavior in a tissue context without presuming specialized programming skills.
Results: We developed a graphical modeling system for multi-agent based simulation of tissue homeostasis. An editor allows the intuitive and hierarchically structured specification of cellular behavior. The models are then automatically compiled into highly efficient source code and dynamically linked to an interactive graphical simulation environment. The system allows the quantitative analysis of the morphological and functional tissue properties emerging from the cell behavioral model. We demonstrate the relevance of the approach using a recently published model of epidermal homeostasis as well as a series of cell-cycle models.
Availability: The complete software is available in binary executables for MS-Windows and Linux at tiga.uni-hd.de
Contact: niels.grabe@bioquant.uni-heidelberg.de
A statistical framework for protein quantitation in bottom-up MS-based proteomics
Authors: Karpievitch Yuliya , Stanley Jeff , Taverner Thomas , Huang Jianhua , Adkins Joshua N. , Ansong Charles , Heffron Fred , Metz Thomas O. , Qian Wei-Jun , Yoon Hyunjin , Smith Richard D. , Dabney Alan R. 
Published: June 2009

AbstractMotivation: Quantitative mass spectrometry-based proteomics requires protein-level estimates and associated confidence measures. Challenges include the presence of low quality or incorrectly identified peptides and informative missingness. Furthermore, models are required for rolling peptide-level information up to the protein level.Results: We present a statistical model that carefully accounts for informative missingness in peak intensities and allows unbiased, model-based, protein-level estimation and inference. The model is applicable to both label-based and label-free quantitation experiments. We also provide automated, model-based, algorithms for filtering of proteins and peptides as well as imputation of missing values. Two LC/MS datasets are used to illustrate the methods. In simulation studies, our methods are shown to achieve substantially more discoveries than standard alternatives.Availability: The software has been made available in the open-source proteomics platform DAnTE (http://omics.pnl.gov/software/).Contact: adabney@stat.tamu.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy
Authors: Liu Xiaowen , Han Yonghua , Yuen Denis , Ma Bin 
Published: June 2009

Abstract
Motivation: The bottom-up tandem mass spectrometry (MS/MS) is regularly used in proteomics nowadays for identifying proteins from a sequence database. De novo sequencing software is also available for sequencing novel peptides with relatively short sequence lengths. However, automated sequencing of novel proteins from MS/MS remains a challenging problem.
Results: Very often, although the target protein is novel, it has a homologous protein included in a known database. When this happens, we propose a novel algorithm and automated software tool, named Champs, for sequencing the complete protein from MS/MS data of a few enzymatic digestions of the purified protein. Validation with two standard proteins showed that our automated method yields &gt;99% sequence coverage and 100% sequence accuracy on these two proteins. Our method is useful to sequence novel proteins or ‘re-sequence’ a protein that has mutations comparing with the database protein sequence.
Availability: The software, named Champs (Complete Homology-Assisted Ms/ms Protein Sequencing), and the MS/MS data used in the article, are freely available at http://monod.uwaterloo.ca/champs/.
Contact: binma@uwaterloo.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Reliable prediction of protein thermostability change upon double mutation from amino acid sequence
Authors: Huang Liang-Tsung , Gromiha M. Michael 
Published: June 2009

Abstract
Summary: The accurate prediction of protein stability change upon mutation is one of the important issues for protein design. In this work, we have focused on the stability change of double mutations and systematically analyzed the wild-type and mutant residues, patterns in amino acid sequence and locations of mutants. Based on the sequence information of wild-type, mutant and three neighboring residues, we have presented a weighted decision table method (WET) for predicting the stability changes of 180 double mutants obtained from thermal (ΔΔG) denaturation. Using 10-fold cross-validation test, our method showed a correlation of 0.75 between experimental and predicted values of stability changes, and an accuracy of 82.2% for discriminating the stabilizing and destabilizing mutants.
Availability: http://bioinformatics.myweb.hinet.net/wetstab.htm
Contact: michael-gromiha@aist.go.jp
Supplementary information: Supplementary data are available at Bioinformatics online.