bluuebunny/crossref_metadata_2025_split huggingface dataset:
The palliative care needs for fibrotic interstitial lung disease: A qualitative study of patients, informal caregivers and health professionals
Authors: Bajwah Sabrina , Higginson Irene J , Ross Joy R , Wells Athol U , Birring Surinder S , Riley Julia , Koffman Jonathan 
Published: July 2013

Background: While there have been some studies looking at the impact on quality of life of patients with idiopathic pulmonary fibrosis, to date no qualitative research looking at the specialist palliative needs of these patients has been conducted. Aim: This study aims to explore the specialist palliative care needs of people living with end-stage progressive idiopathic fibrotic interstitial lung disease. Design and settings/participants: In total, 18 qualitative semi-structured in-depth interviews were conducted with patients, their informal caregivers and health professionals across two specialist interstitial lung disease centres in London and in the community. Results: Many participants reported uncontrolled symptoms of shortness of breath, cough and insomnia, which profoundly impacted every part of patients’ and informal caregivers’ lives. Psychologically, patients were frustrated and angry at the way in which their illness severely limited their ability to engage in activities of daily living and compromised their independence. Furthermore, both patients and informal caregivers also reported that the disease seriously affected family relationships where strain was pronounced. There was varied knowledge and confidence among health professionals in managing symptoms, and psychosocial needs were often underestimated. Conclusion: This study is the first of its kind to examine in depth the impact of symptoms and psychosocial needs revealing the profound effect on every aspect of progressive idiopathic fibrotic interstitial lung disease patients’ and informal caregivers’ lives. Education and guidance of appropriate palliative care interventions to improve symptom control are needed. A case conference intervention with individualised care plans may help in addressing the substantial symptom control and psychosocial needs of these patients and informal caregivers.
Use of Magnetic Resonance Arthrography to Compare Clinical Features and Structural Integrity After Arthroscopic Repair of Bursal Versus Articular Side Partial-Thickness Rotator Cuff Tears
Authors: Kim Sung-Jae , Kim Sung-Hwan , Lim Su-Han , Chun Yong-Min 
Published: July 2013

Background: There has been no study using magnetic resonance arthrography (MRA) to compare clinical features and structural integrity after arthroscopic repair of bursal and articular side partial-thickness rotator cuff tears (PTRCTs). Hypothesis: The 2 groups studied, which consisted of patients who underwent arthroscopic repair for either the articular side or the bursal side, would show significant improvement in overall outcomes after surgery, even though clinical outcomes and structural integrity would not be significantly different. It was thought that the incidence of preoperative positive impingement signs and protruded spurs on the acromion undersurface would be higher in patients with a bursal side tear. Study Design: Case-control study; Level of evidence, 3. Methods: The current study consisted of 83 patients who underwent arthroscopic repair for either articular side (group A; n = 29) or bursal side (group B; n = 54) PTRCT and who were available at the 2-year follow-up. Clinical outcomes were compared by use of the Neer impingement sign, visual analog scale for pain, Simple Shoulder Test, University of California Los Angeles score, and American Shoulder and Elbow Surgeons score. At 6 months after surgery, MRA was used to assess structural integrity. Results: At 2-year follow-up, both groups showed significant improvement in pain and shoulder function scores, even though there was no significant difference between groups. The retear rate on follow-up MRA was not significantly different between group A (8%) and B (11%). Patients in group B, compared with group A, showed a higher incidence of the preoperative impingement sign (89% vs 52%, respectively; P = .004), protruded spur on the acromion undersurface (69% vs 0%, respectively; P < .001), and concomitant acromioplasty (93% vs 24%, respectively; P < .001). Conclusion: Both articular and bursal side PTRCTs showed significant functional improvements after arthroscopic repair. The bursal side tears had a higher incidence of impingement sign at preoperative examination and more often had a protruded spur on the acromion undersurface.
A review of the concepts, terminologies and dilemmas in the assessment of decisional capacity: a focus on alcoholism
Authors: Restifo Sam 
Published: July 2013

Objective: The formal assessment of a person’s capacity for making reasoned decisions is an infrequent and usually unappealing clinical task. The purpose of this paper is to dissect the task, consider the component parts, clarify those aspects that can be problematic and highlight those that remain so. Method: The paper reviews the concepts, terminologies and dilemmas around alcoholism, insight, lack of insight, denial, judgement, will, decisional capacity and competence. Conclusion: Assessments of patients suffering from alcoholism (or any other dyscontrol problem such as deliberate self-harm, problem gambling or eating disorders) are likely to evoke unease because of the interweaving of potentially disputable phenomenological, clinical, ethical, semantic and legal aspects. Familiarity with the concepts and terms around decisional capacity helps to orientate clinicians in their work. There remain some particular conceptual issues that are in need of further scholarly attention.
The response of structures equipped with tuned liquid dampers of complex geometry
Authors: Love JS , Tait MJ 
Published: July 2013

Tuned liquid dampers (TLDs) employ sloshing fluid to reduce the resonant response of structures. Existing structure-TLD models are limited to rectangular or circular tanks, shapes that may not always be feasible in practice due to geometric restrictions of the building floor plan. This paper utilizes an equivalent linearized mechanical model and a nonlinear multimodal model to predict the response of the structure-TLD systems where the TLD tank geometry is irregular. Experimental structure-TLD system tests are conducted that consider two irregular tank shapes. Response history plots and frequency response plots of the structural displacement and TLD wave heights are created to evaluate the models using the experimental results. The parent distributions and 10-minute peak distributions of the structural displacements and TLD wave heights are created for the simulated and experimental results. These distributions indicate that both the linearized and nonlinear models can accurately predict the structural response; however, the linearized model substantially underestimates the peak wave heights. Since wave heights are required to establish the required tank free board, or roof impact pressures, it is concluded that nonlinear analysis of the structure-TLD system model is required before a TLD design is finalized.
Detection of phase-dependent transcriptomic changes and Rubisco-mediated CO2 fixation into poly (3-hydroxybutyrate) under heterotrophic condition in Ralstonia eutropha H16 based on RNA-seq and gene deletion analyses
Authors: Shimizu Rie , Chou Kenta , Orita Izumi , Suzuki Yutaka , Nakamura Satoshi , Fukui Toshiaki 
Published: July 2013

Abstract

Background

Ralstonia eutropha H16 is well known to produce polyhydroxyalkanoates (PHAs), which are potential bio-based biodegradable plastics, in an efficient manner as an energy storage material under unbalanced growth conditions. To obtain further knowledge of PHA biosynthesis, this study performed a quantitative transcriptome analysis based on deep sequencing of the complementary DNA generated from the RNA (RNA-seq) of R. eutropha H16.

Results
Total RNAs were extracted from R. eutropha cells in growth, PHA production, and stationary phases on fructose. rRNAs in the preparation were removed by repeated treatments with magnetic beads specific to bacterial rRNAs, and then the 36 bp sequences were determined using an Illumina high-throughput sequencer. The RNA-seq results indicated the induction of gene expression for transcription, translation, cell division, peptidoglycan biosynthesis, pilus and flagella assembly, energy conservation, and fatty acid biosynthesis in the growth phase; and the repression trends of genes involved in central metabolisms in the PHA production phase. Interestingly, the transcription of genes for Calvin-Benson-Bassham (CBB) cycle and several genes for β-oxidation were significantly induced in the PHA production phase even when the cells were grown on fructose. Moreover, incorporation of 13C was observed in poly(3-hydroxybutyrate) synthesized by R. eutropha H16 from fructose in the presence of NaH13CO3, and further gene deletion analyses revealed that both of the two ribulose 1,5-bisphosphate carboxylase (Rubiscos) in CBB cycle were actually functional in CO2 fixation under the heterotrophic condition.

Conclusions
The results revealed the phase-dependent transcriptomic changes and a CO2 fixation capability under heterotrophic conditions by PHA-producing R. eutropha.
Designing a multifaceted survivorship care plan to meet the information and communication needs of breast cancer patients and their family physicians: results of a qualitative pilot study
Authors: Haq Rashida , Heus Lineke , Baker Natalie A , Dastur Daisy , Leung Fok-Han , Leung Eman , Li Benjamin , Vu Kathy , Parsons Janet A 
Published: July 2013

Abstract

Background
Following the completion of treatment and as they enter the follow-up phase, breast cancer patients (BCPs) often recount feeling ‘lost in transition’, and are left with many questions concerning how their ongoing care and monitoring for recurrence will be managed. Family physicians (FPs) also frequently report feeling ill-equipped to provide follow-up care to BCPs. In this three-phase qualitative pilot study we designed, implemented and evaluated a multi-faceted survivorship care plan (SCP) to address the information needs of BCPs at our facility and of their FPs.

Methods
In Phase 1 focus groups and individual interviews were conducted with 35 participants from three stakeholder groups (BCPs, FPs and oncology specialist health care providers (OHCPs)), to identify specific information needs. An SCP was then designed based on these findings, consisting of both web-based and paper-based tools (Phase 2). For Phase 3, both sets of tools were subsequently evaluated via focus groups and interviews with 26 participants. Interviews and focus groups were audio taped, transcribed and content analysed for emergent themes and patterns.

Results
In Phase 1 patients commented that web-based, paper-based and human resources components were desirable in any SCP. Patients did not focus exclusively on the post-treatment period, but instead spoke of evolving needs throughout their cancer journey. FPs indicated that any tools to support them must distill important information in a user-friendly format. In Phase 2, a pilot SCP was subsequently designed, consisting of both web-based and paper-based materials tailored specifically to the needs of BCPs as well as FPs. During Phase 3 (evaluation) BCPs indicated that the SCP was effective at addressing many of their needs, and offered suggestions for future improvements. Both patients and FPs found the pilot SCP to be an improvement from the previous standard of care. Patients perceived the quality of the BCP-FP relationship as integral to their comfort with FPs assuming follow-up responsibilities.

Conclusions
This pilot multi-component SCP shows promise in addressing the information needs of BCPs and the FPs who care for them. Next steps include refinement of the different SCP components, further evaluation (including usability testing), and planning for more extensive implementation.
Direct observation of CD4 T cell morphologies and their cross-sectional traction force derivation on quartz nanopillar substrates using focused ion beam technique
Authors: Kim Dong-Joo , Kim Gil-Sung , Hyung Jung-Hwan , Lee Won-Yong , Hong Chang-Hee , Lee Sang-Kwon 
Published: July 2013

Abstract
Direct observations of the primary mouse CD4 T cell morphologies, e.g., cell adhesion and cell spreading by culturing CD4 T cells in a short period of incubation (e.g., 20 min) on streptavidin-functionalized quartz nanopillar arrays (QNPA) using a high-content scanning electron microscopy method were reported. Furthermore, we first demonstrated cross-sectional cell traction force distribution of surface-bound CD4 T cells on QNPA substrates by culturing the cells on top of the QNPA and further analysis in deflection of underlying QNPA via focused ion beam-assisted technique.
Heterogeneous susceptibility of circulating SIV isolate capsids to HIV-interacting factors
Authors: Mamede João I , Sitbon Marc , Battini Jean-Luc , Courgnaud Valérie 
Published: July 2013

Abstract

Background
Many species of non-human primates in Africa are naturally infected by simian immunodeficiency viruses (SIV) and humans stand at the forefront of exposure to these viruses in Sub-Saharan Africa. Cross-species transmission and adaptation of SIV to humans have given rise to human immunodeficiency viruses (HIV-1 and HIV-2) on twelve accountable, independent occasions. However, the determinants contributing to a simian-to-human lasting transmission are not fully understood. Following entry, viral cores are released into the cytoplasm and become the principal target of host cellular factors. Here, we evaluated cellular factors likely to be involved in potential new SIV cross-species transmissions. We investigated the interactions of capsids from naturally circulating SIV isolates with both HIV-1 restricting (i.e. TRIM5 proteins) and facilitating (i.e. cyclophilin A and nucleopore-associated Nup358/RanBP2 and Nup153) factors in single-round infectivity assays that reproduce early stages of the viral life-cycle.

Results
We show that human TRIM5α is unlikely to prevent cross-species transmission of any SIV we tested and observed that the SIV CA-CypA interaction is a widespread but not a universal feature. Moreover, entry in the nucleus of different SIV appeared to follow pathways that do not necessarily recruit Nup358/RanBP2 or Nup153, and this regardless of their interaction with CypA. Nevertheless, we found that, like HIV-1, human-adapted HIV-2 infection was dependent on Nup358/RanBP2 and Nup153 interactions for optimal infection. Furthermore, we found that, unlike HIV CA, SIV CA did not require a direct interaction with the Cyp-like domain of Nup358/RanBP2 to carry out successful infection.

Conclusions
Circulating SIV present a variety of phenotypes with regard to CA-interacting restricting or facilitating factors. Altogether, we unveiled unidentified pathways for SIV CA, which could also be exploited by HIV in different cellular contexts, to drive entry into the nucleus. Our findings warrant a closer evaluation of other potential defenses against circulating SIV.
Differences in learning rates for item and associative memories between amnestic mild cognitive impairment and healthy controls
Authors: Wang Pengyun , Li Juan , Li Huijie , Zhang Shouzi 
Published: July 2013

AbstractBackgroundIt has been established that the overall performance of associative memory was disproportionately impaired in contrast to item memory in aMCI (Amnestic mild cognitive impairment) patients, but little is known about the specific aspects of the memory process that show differences between aMCI and healthy controls. By comparing an item-item associative learning test with an individual item learning test, the present study investigated whether the rate of learning was slower in associative memory than in item memory in aMCI. Furthermore, we examined whether deficits in intertrial acquisition and consolidation contributed to the potential disproportionate impairments in the learning rate of associative memory for aMCI patients. In addition, we further explored whether the aMCI-discriminative power of the associative memory test increases more than that of the item memory test when the number of learning-test trials increases.MethodsA group of 40 aMCI patients and 40 matched control participants were administered a standardized item memory test (Auditory Verbal Learning Test, AVLT) and a standardized associative memory test (Paired Associative Learning Test, PALT), as well as other neuropsychological tests and clinical assessments.ResultsThe results indicated that the learning rate deficits in aMCI patients were more obvious for associative memory than for item memory and that the deficits resulted from impairments in both intertrial acquisition and consolidation. In addition, the receiver operating characteristic curve and logistical regression analysis revealed that the discriminative power of the associative memory test for aMCI was larger than that of the item memory test, especially with more than one learning-test trials.ConclusionsDue to more deficits in learning rate of associative memory than that of item memory, the discriminative power for aMCI tended to be larger in associative memory than in item memory when the number of learning-test trials increased. It is suggested that associative memory tests with multiple trials may be particularly useful for early detection of aMCI.
Risk factors for the transmission of foot-and-mouth disease during the 2010 outbreak in Japan: a case–control study
Authors: Muroga Norihiko , Kobayashi Sota , Nishida Takeshi , Hayama Yoko , Kawano Takaaki , Yamamoto Takehisa , Tsutsui Toshiyuki 
Published: July 2013

Abstract

Background
In 2010, foot-and-mouth disease (FMD) occurred for the first time in a decade in Japan. Movement or shipment of people and animals around infected farms was restricted; however these contingency measures proved insufficient to prevent FMD spread. Consequently, a total of 292 farms were confirmed as infected during this outbreak. We conducted a case–control study to identify the risk factors associated with FMD transmission between farms during these restrictions. As there was discordance in the control measures taken, risk factors were examined separately for two areas. Analyses were also performed separately for cattle and pig farms given their different infectivity and susceptibility.

Results
For cattle farms in the movement restriction area, the odds of having the factor ‘farm equipment was shared with other farms’ was significantly higher for case farms than for control farms. For cattle farms in the shipment restriction area, the odds of having the factors ‘feed transport vehicles visited the farm’ and ‘staff of livestock-related companies visited the farm’ were significantly higher on case farms than control farms. In pig farms in the movement restriction area, the odds of having factor ‘farm staff commuted from outside’ was 20 times higher for case farms than control farms. In addition, case farms were less likely to have the factors ‘fattening farm’ and ‘barn has physical barriers’ compared with control farms.

Conclusions
In the movement restriction area, the disease was likely to spread regardless of the movement of people and vehicles, and physical barriers were found to be a protective factor. Therefore, physical barriers from the surrounding environments seemed to prevent farms from being infected. Conversely, in the shipment restriction area, movement of people and vehicles was strongly associated with disease spread. These results allow a better understanding of the risk factors associated with FMD transmission and are useful to enhance future preventive measures against transmission during FMD outbreaks.
Creation of RTOG compliant patient CT-atlases for automated atlas based contouring of local regional breast and high-risk prostate cancers
Authors: Velker Vikram M , Rodrigues George B , Dinniwell Robert , Hwee Jeremiah , Louie Alexander V 
Published: July 2013

Abstract

Background
Increasing use of IMRT to treat breast and prostate cancers at high risk of regional nodal spread relies on accurate contouring of targets and organs at risk, which is subject to significant inter- and intra-observer variability. This study sought to evaluate the performance of an atlas based deformable registration algorithm to create multi-patient CT based atlases for automated contouring.

Methods
Breast and prostate multi-patient CT atlases (n = 50 and 14 respectively) were constructed to be consistent with RTOG consensus contouring guidelines. A commercially available software algorithm was evaluated by comparison of atlas-predicted contours against manual contours using Dice Similarity coefficients.

Results
High levels of agreement were demonstrated for prediction of OAR contours of lungs, heart, femurs, and minor editing required for the CTV breast/chest wall. CTVs generated for axillary nodes, supraclavicular nodes, prostate, and pelvic nodes demonstrated modest agreement. Small and highly variable structures, such as internal mammary nodes, lumpectomy cavity, rectum, penile bulb, and seminal vesicles had poor agreement.

Conclusions
A method to construct and validate performance of CT-based multi-patient atlases for automated atlas based auto-contouring has been demonstrated, and can be adopted for clinical use in planning of local regional breast and high-risk prostate radiotherapy.
DCJ-indel and DCJ-substitution distances with distinct operation costs
Authors: da Silva Poly H , Machado Raphael , Dantas Simone , Braga Marília DV 
Published: July 2013

Abstract

Background
Classical approaches to compute the genomic distance are usually limited to genomes with the same content and take into consideration only rearrangements that change the organization of the genome (i.e. positions and orientation of pieces of DNA, number and type of chromosomes, etc.), such as inversions, translocations, fusions and fissions. These operations are generically represented by the double-cut and join (DCJ) operation. The distance between two genomes, in terms of number of DCJ operations, can be computed in linear time. In order to handle genomes with distinct contents, also insertions and deletions of fragments of DNA – named indels – must be allowed. More powerful than an indel is a substitution of a fragment of DNA by another fragment of DNA. Indels and substitutions are called content-modifying operations. It has been shown that both the DCJ-indel and the DCJ-substitution distances can also be computed in linear time, assuming that the same cost is assigned to any DCJ or content-modifying operation.

Results
In the present study we extend the DCJ-indel and the DCJ-substitution models, considering that the content-modifying cost is distinct from and upper bounded by the DCJ cost, and show that the distance in both models can still be computed in linear time. Although the triangular inequality can be disrupted in both models, we also show how to efficiently fix this problem a posteriori.