bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probabilistic modeling and analysis of the effects of extra-cellular matrix density on the sizes, shapes, and locations of integrin clusters in adherent cells
Authors: Welf Erik S , Naik Ulhas P , Ogunnaike Babatunde A 
Published: August 2011

Abstract

Background
Regulation of integrin binding to the specific complementary sites on extra-cellular matrix (ECM) proteins plays a major role in cell adhesion and migration. In addition to regulating single integrin-ligand bonds by affinity modulation, cells regulate their adhesiveness by forming integrin clusters. Although it is clear that cells exhibit different adhesion and migration behaviors on surfaces coated with different concentrations of ECM proteins, it is not clear if this response is mediated by changes in the availability of integrin binding sites or by differential intracellular signaling that may affect integrin binding and clustering.

Results
To quantify how the concentration of ECM affects integrin clustering, we seeded cells expressing the integrin αIIbβ3 on different concentrations of the complementary ECM protein fibrinogen (Fg) and measured the resulting integrin cluster properties. We observed heterogeneity in the properties of integrin clusters, and to characterize this population heterogeneity we use a probabilistic modeling approach to quantify changes to the distributions of integrin cluster size, shape, and location.

Conclusions
Our results indicate that in response to increasing ECM density cells form smaller integrin clusters that are less elongated and closer to the cell periphery. These results suggest that cells can sense the availability of ECM binding sites and consequently regulate integrin clustering as a function of ECM density.
Harnessing the self-harvesting capability of benthic cyanobacteria for use in benthic photobioreactors
Authors: Esson Diane , Wood Susanna A , Packer Michael A 
Published: August 2011

Abstract
Benthic species of algae and cyanobacteria (i.e., those that grow on surfaces), may provide potential advantages over planktonic species for some commercial-scale biotechnological applications. A multitude of different designs of photobioreactor (PBR) are available for growing planktonic species but to date there has been little research on PBR for benthic algae or cyanobacteria. One notable advantage of some benthic cyanobacterial species is that during their growth cycle they become positively buoyant, detach from the growth surface and form floating mats. This 'self-harvesting' capability could be advantageous in commercial PBRs as it would greatly reduce dewatering costs. In this study we compared the growth rates and efficiency of 'self-harvesting' among three species of benthic cyanobacteria; Phormidium autumnale; Phormidium murrayi and Planktothrix sp.. Phormidium autumnale produced the greatest biomass and formed cohesive mats once detached. Using this strain and an optimised MLA media, a variety of geometries of benthic PBRs (bPBRs) were trialed. The geometry and composition of growth surface had a marked effect on cyanobacterial growth. The highest biomass was achieved in a bPBR comprising of a vertical polyethylene bag with loops of silicone tubing to provide additional growth surfaces. The productivity achieved in this bPBR was a similar order of magnitude as planktonic species, with the additional advantage that towards the end of the exponential phase the bulk of the biomass detached forming a dense mat at the surface of the medium.
Decreased catalytic function with altered sumoylation of DNA topoisomerase I in the nuclei of scleroderma fibroblasts
Authors: Zhou Xiaodong , Lin Wei , Tan Filemon K , Assassi Shervin , Fritzler Mavin J , Guo Xinjian , Sharif Roozbeh , Xia Tom , Lai Syeling , Arnett Frank C 
Published: August 2011

Abstract
Introduction
Sumoylation is involved in nucleolus-nucleoplasm transport of DNA topoisomerase I (topo I), which may associate with changes of cellular and topo I functions. Skin fibroblasts of patients with systemic sclerosis (SSc) exhibit profibrotic cellular changes. The aims of this study were to examine the catalytic function and sumoylation of topo I in the nuclei of SSc fibroblasts, a major cell type involved in the fibrotic process.

Methods
Eleven pairs of fibroblast strains obtained from nonlesional skin biopsies of SSc patients and age/sex/ethnicity-matched normal controls were examined for catalytic function of nuclear topo I. Immunoprecipitation (IP)-Western blots were used to examine sumoylation of fibroblast topo I. Real-time quantitative RT-PCR was used to measure transcript levels of SUMO1 and COL1A2 in the fibroblasts.

Results
Topo I in nuclear extracts of SSc fibroblasts generally showed a significantly lower efficiency than that of normal fibroblasts in relaxing equivalent amounts of supercoiled DNA. Increased sumoylation of topo I was clearly observed in 7 of 11 SSc fibroblast strains. Inhibition of SUMO1 with SUMO1 siRNA improved the catalytic efficiency of topo I in the SSc fibroblasts. In contrast, sumoylation of recombinant topo I proteins reduced their catalytic function.

Conclusions
The catalytic function of topo I was decreased in SSc fibroblasts, to which increased sumoylation of topo I may contribute.
Managing daily intensive care activities: An observational study concerning ad hoc decision making of charge nurses and intensivists
Authors: Lundgrén-Laine Heljä , Kontio Elina , Perttilä Juha , Korvenranta Heikki , Forsström Jari , Salanterä Sanna 
Published: August 2011

Abstract
Introduction
Management of daily activities in ICUs is challenging. ICU shift leaders, charge nurses and intensivists have to make several immediate ad hoc decisions to enable the fluent flow of ICU activities. Even though the management of ICU activities is quite well delineated by international consensus guidelines, we know only a little about the content of the real clinical decision making of ICU shift leaders.

Methods
We conducted an observational study with the think-aloud technique to describe the ad hoc decision making of ICU shift leaders. The study was performed in two university-affiliated hospital ICUs. Twelve charge nurses and eight intensivists were recruited. Observations were recorded and transcribed for qualitative content analysis using the protocol analysis method. The software program NVivo 7 was used to manage the data. The interrater agreement was assessed with percentages and by Cohen's κ.

Results
We identified 463 ad hoc decisions made by the charge nurses and 444 made by the intensivists. During our data collection time, this breaks down to over 230 immediately made decisions per day (24 hours). We divided the ad hoc decision making of ICU shift leaders into two types: process-focused and situation-focused. Process-focused decision making included more permanent information, such as human resources, know-how and material resources, whereas situation-focused decision making included decisions about single events, such as patient admission. We named eight different categories for ICU ad hoc decision making: (1) adverse events, (2) diagnostics, (3) human resources and know-how, (4) material resources, (5) patient admission, (6) patient discharge, (7) patient information and vital signs and (8) special treatments.

Conclusions
ICU shift leaders make a great number of complex ad hoc decisions throughout the day. Often this decision making involves both intensivists and charge nurses. It forms a bundle that requires versatile, immediate information for a successful outcome. In the future, we need to investigate which information is crucial for ad hoc decision making. These challenges should also be emphasised when information technology programs for ICU care management are developed.
Specific Training Program Improves Oncologists' Palliative Care Communication Skills in a Randomized Controlled Trial
Authors: Goelz Tanja , Wuensch Alexander , Stubenrauch Sara , Ihorst Gabriele , de Figueiredo Marcelo , Bertz Hartmut , Wirsching Michael , Fritzsche Kurt 
Published: August 2011

PurposeThe aim of the study was to demonstrate that COM-ON-p, concise and individualized communication skills training (CST), improves oncologists' communication skills in consultations focusing on the transition to palliative care.MethodsForty-one physicians were randomly assigned to a control (CG) or intervention group (IG). At t0, all physicians held two video-recorded consultations with actor-patient pairs. Afterward, physicians in the IG participated in COM-ON-p. Five weeks after t0, a second assessment took place (t1). COM-ON-p consists of an 11-hour workshop (1.5 days), pre- and postassessment (2 hours), and coaching (0.5 hours). Physicians focused on practicing individual learning goals with actor patients in small groups. To evaluate the training, blinded raters assessed communication behavior of the physicians in video-recorded actor-patient consultations using a specific checklist. Data were analyzed using a mixed model with baseline levels as covariates.ResultsParticipants in the IG improved significantly more than those in the CG in all three sections of the COM-ON-Checklist: skills specific to the transition to palliative care, global communication skills, and involvement of significant others (all P < .01). Differences between the CG and IG on the global items of communication skills and involvement of significant others were also significant (P < .01). Effect sizes were medium to large, with a 0.5-point improvement on average on a five-point rating scale.ConclusionPhysicians can be trained to meet better core challenges during the transition to palliative care through developed concise CST. Generalization and transfer into clinical practice must be proven in additional studies.
Natural Course of Insomnia Comorbid With Cancer: An 18-Month Longitudinal Study
Authors: Savard Josée , Ivers Hans , Villa Julie , Caplette-Gingras Aude , Morin Charles M. 
Published: August 2011

Purpose This study aimed to assess the prevalence and natural course (incidence, persistence, remission, and relapse) of insomnia comorbid with cancer during an 18-month period. Patients and Methods All patients scheduled to receive a curative surgery for a first diagnosis of nonmetastatic cancer were approached on the day of their preoperative visit to participate in the study. A total of 962 patients with cancer (mixed sites) completed an insomnia diagnostic interview at the perioperative phase (T1), as well as at 2 (T2), 6 (T3) 10 (T4), 14 (T5), and 18 (T6) months after surgery. Results Findings revealed high rates of insomnia at baseline (59%), including 28% with an insomnia syndrome. The prevalence of insomnia generally declined over time but remained pervasive even at the end of the 18-month period (36%). Rates were greater in patients with breast (42% to 69%) and gynecologic (33% to 68%) cancer and lower in men with prostate cancer (25% to 39%) throughout the study. Nearly 15% of patients had a first incidence of insomnia during the study, and 19.5% experienced relapse. The evolution of symptoms varied according to sleep status. Remissions (patients becoming good sleepers) were much less likely for patients with an insomnia syndrome (10.8% to 14.9%) than for those with insomnia symptoms (42.0% to 51.3%). Most frequently (37.6%), patients with an insomnia syndrome at baseline kept that status throughout the 18-month period. Conclusion Insomnia is a frequent and enduring problem in patients with cancer, particularly at the syndrome level. Early intervention strategies, such as cognitive-behavioral therapy, could prevent the problem from becoming more severe and chronic.
Clinical Features and Outcome of Patients With Non–Small-Cell Lung Cancer Harboring BRAF Mutations
Authors: Marchetti Antonio , Felicioni Lara , Malatesta Sara , Grazia Sciarrotta Maria , Guetti Luigi , Chella Antonio , Viola Patrizia , Pullara Carmela , Mucilli Felice , Buttitta Fiamma 
Published: August 2011

Purpose To investigate the prevalence, distribution, and prognostic role of BRAF mutations in a large cohort of white patients with non–small-cell lung cancer (NSCLC). Patients and Methods A retrospective series of 1,046 NSCLCs—comprising 739 adenocarcinomas (ADCs) and 307 squamous cell carcinomas (SCCs)—was investigated for BRAF mutations. High-resolution melting analysis followed by sequencing and strip hybridization assay were used. All patients were also analyzed for KRAS and EGFR mutations. Results BRAF mutations were present in 36 ADCs (4.9%) and one SCC (0.3%; P = .001). Twenty-one of the mutations (56.8%) were V600E, and 16 (43.2%) were non-V600E. V600E mutations were significantly more prevalent in females (16 of 187 patients; 8.6%) than in males (five of 552 patients; 0.9%), as indicated by multivariate logistic regression analysis (hazard ratio [HR], 11.29; P < .001). V600E-mutated tumors showed an aggressive histotype characterized by micropapillary features in 80% of patients and were significantly associated with shorter disease-free and overall survival rates on both univariate (HR, 2.67; P < .001 and HR, 2.97; P < .001, respectively) and multivariate analyses (HR, 2.19; P = .011 and HR, 2.18; P = .014, respectively). All non-V600E mutations were found in smokers (P = .015) and were associated with neither clinicopathologic parameters nor prognosis. BRAF and EGFR were concomitantly mutated in two tumors. Conclusion We report for the first time to our knowledge that V600E and non-V600E BRAF mutations affect different patients with NSCLC. V600E mutations are significantly associated with female sex and represent a negative prognostic factor. In addition, we identified a number of other clinicopathologic parameters potentially useful for the selection of patients carrying BRAF mutations.
Inflammation and Behavioral Symptoms After Breast Cancer Treatment: Do Fatigue, Depression, and Sleep Disturbance Share a Common Underlying Mechanism?
Authors: Bower Julienne E. , Ganz Patricia A. , Irwin Michael R. , Kwan Lorna , Breen Elizabeth C. , Cole Steve W. 
Published: August 2011

Purpose Fatigue, depression, and sleep disturbance are common adverse effects of cancer treatment and frequently co-occur. However, the possibility that inflammatory processes may underlie this constellation of symptoms has not been examined. Patients and Methods Women (N = 103) who had recently finished primary treatment (ie, surgery, radiation, chemotherapy) for early-stage breast cancer completed self-report scales and provided blood samples for determination of plasma levels of inflammatory markers: soluble tumor necrosis factor (TNF) receptor II (sTNF-RII), interleukin-1 receptor antagonist, and C-reactive protein. Results Symptoms were elevated at the end of treatment; greater than 60% of participants reported clinically significant problems with fatigue and sleep, and 25% reported elevated depressive symptoms. Women treated with chemotherapy endorsed higher levels of all symptoms and also had higher plasma levels of sTNF-RII than women who did not receive chemotherapy (all P < .05). Fatigue was positively associated with sTNF-RII, particularly in the chemotherapy-treated group (P < .05). Depressive symptoms and sleep problems were correlated with fatigue but not with inflammatory markers. Conclusion This study confirms high rates of behavioral symptoms in breast cancer survivors, particularly those treated with chemotherapy, and indicates a role for TNF-α signaling as a contributor to postchemotherapy fatigue. Results also suggest that fatigue, sleep disturbance, and depression may stem from distinct biologic processes in post-treatment survivors, with inflammatory signaling contributing relatively specifically to fatigue.
Structural and biochemical properties of Sept7, a unique septin required for filament formation
Authors: Zent Eldar , Vetter Ingrid , Wittinghofer Alfred 
Published: August 2011

Abstract
Septins constitute a family of conserved guanine nucleotide binding proteins found in a wide range of organisms from fungi to mammals. Members of the family share a canonical G-domain with N- and C-terminal extensions. G-domains assemble into hetero-oligomeric complexes which form non-polarised filaments or rings. Linear filaments are formed between the G-domains using either the guanine nucleotide binding site (G interface) or N- and C-terminal extensions (NC interface). Sept7 is a unique among the 13 human septins in that it occupies the ends of hexameric building blocks which assemble into non-polarised filaments. To gain insight into its particular properties we performed structural and biochemical studies on Sept7. We solved the crystal structure of a Sept7 dimer in the GDP-bound state. The structure and biochemistry of Sept7 provide new insights into the dynamics of the G interface and outline the differences in the properties of Sept7 compared to the members of group 2 septins.
Evidence that a septin diffusion barrier is dispensable for cytokinesis in budding yeast
Authors: Wloka Carsten , Nishihama Ryuichi , Onishi Masayuki , Oh Younghoon , Hanna Julia , Pringle John R. , Krauß Michael , Bi Erfei 
Published: August 2011

Abstract
Septins are essential for cytokinesis in Saccharomyces cerevisiae, but their precise roles remain elusive. Currently, it is thought that before cytokinesis, the hourglass-shaped septin structure at the mother-bud neck acts as a scaffold for assembly of the actomyosin ring (AMR) and other cytokinesis factors. At the onset of cytokinesis, the septin hourglass splits to form a double ring that sandwiches the AMR and may function as diffusion barriers to restrict diffusible cytokinesis factors to the division site. Here, we show that in cells lacking the septin Cdc10 or the septin-associated protein Bud4, the septins form a ring-like structure at the mother-bud neck that fails to re-arrange into a double ring early in cytokinesis. Strikingly, AMR assembly and constriction, the localization of membrane-trafficking and extracellular-matrix-remodeling factors, cytokinesis, and cell-wall-septum formation all occur efficiently in cdc10Δ and bud4Δ mutants. Thus, diffusion barriers formed by the septin double ring do not appear to be critical for S. cerevisiae cytokinesis. However, an AMR mutation and a septin mutation have synergistic effects on cytokinesis and the localization of cytokinesis proteins, suggesting that tethering to the AMR and a septin diffusion barrier may function redundantly to localize proteins to the division site.
Septin9 is involved in septin filament formation and cellular stability
Authors: Füchtbauer Annette , Lassen Louise B. , Jensen Astrid B. , Howard Jennifer , Quiroga Adán de Salas , Warming Søren , Sørensen Annette B. , Pedersen Finn S. , Füchtbauer Ernst-Martin 
Published: August 2011

Abstract
Septin9 (Sept9) is a member of the filament-forming septin family of structural proteins and is associated with a variety of cancers and with hereditary neuralgic amyotrophy. We have generated mice with constitutive and conditional Sept9 knockout alleles. Homozygous deletion of Sept9 results in embryonic lethality around day 10 of gestation whereas mice homozygous for the conditional allele develop normally. Here we report the consequences of homozygous loss of Sept9 in immortalized murine embryonic fibroblasts. Proliferation rate was not changed but cells without Sept9 had an altered morphology compared to normal cells, particularly under low serum stress. Abnormal, fragmented, and multiple nuclei were more frequent in cells without Sept9. Cell migration, as measured by gap-filling and filter-invasion assays, was impaired, but individual cells did not move less than wild-type cells. Sept9 knockout cells showed a reduced resistance to hypo-osmotic stress. Stress fiber and vinculin staining at focal adhesion points was less prominent. Long septin filaments stained for Sept7 disappeared. Instead, staining was found in short, often curved filaments and rings. Furthermore, Sept7 was no longer localized to the mitotic spindle. Together, these data reveal the importance of Sept9 for septin filament formation and general cell stability.
ARTS, the unusual septin: structural and functional aspects
Authors: Mandel-Gutfreund Yael , Kosti Idit , Larisch Sarit 
Published: August 2011

Abstract
The human Septin 4 gene (Sept4) encodes two major protein isoforms; Sept4_i1 (H5/PNUTL2) and Sept4_i2/ARTS. Septins have been traditionally studied for their role in cytokinesis and their filament-forming abilities, but subsequently have been implicated in diverse functions, including membrane dynamics, cytoskeletal reorganization, vesicle trafficking, and tumorigenesis. ARTS is localized at mitochondria and promotes programmed cell death (apoptosis). These features distinguish ARTS from any other known human septin family member. This review compares the structural and functional properties of ARTS with other septins. In addition, it describes how a combination of two distinct promoters, differential splicing, and intron retention leads to the generation of two different Sept4 variants with diverse biological activity.
The mother-bud neck as a signaling platform for the coordination between spindle position and cytokinesis in budding yeast
Authors: Merlini Laura , Piatti Simonetta 
Published: August 2011

Abstract
During asymmetric cell division, spindle positioning is critical for ensuring the unequal inheritance of polarity factors. In budding yeast, the mother-bud neck determines the cleavage plane and a correct nuclear division between mother and daughter cell requires orientation of the mitotic spindle along the mother-bud axis. A surveillance device called the spindle position/orientation checkpoint (SPOC) oversees this process and delays mitotic exit and cytokinesis until the spindle is properly oriented along the division axis, thus ensuring genome stability. Cytoskeletal proteins called septins form a ring at the bud neck that is essential for cytokinesis. Furthermore, septins and septin-associated proteins are implicated in spindle positioning and SPOC. In this review, we discuss the emerging connections between septins and the SPOC and the role of the mother-bud neck as a signaling platform to couple proper chromosome segregation to cytokinesis.
Genetic interactions with mutations affecting septin assembly reveal ESCRT functions in budding yeast cytokinesis
Authors: McMurray Michael A. , Stefan Christopher J. , Wemmer Megan , Odorizzi Greg , Emr Scott D. , Thorner Jeremy 
Published: August 2011

Abstract
Membrane trafficking via targeted exocytosis to the Saccharomyces cerevisiae bud neck provides new membrane and membrane-associated factors that are critical for cytokinesis. It remains unknown whether yeast plasma membrane abscission, the final step of cytokinesis, occurs spontaneously following extensive vesicle fusion, as in plant cells, or requires dedicated membrane fission machinery, as in cultured mammalian cells. Components of the endosomal sorting complexes required for transport (ESCRT) pathway, or close relatives thereof, appear to participate in cytokinetic abscission in various cell types, but roles in cell division had not been documented in budding yeast, where ESCRTs were first characterized. By contrast, the septin family of filament-forming cytoskeletal proteins were first identified by their requirement for yeast cell division. We show here that mutations in ESCRT-encoding genes exacerbate the cytokinesis defects of cla4Δ or elm1Δ mutants, in which septin assembly is perturbed at an early stage in cell division, and alleviate phenotypes of cells carrying temperature-sensitive alleles of a septin-encoding gene, CDC10. Elevated chitin synthase II (Chs2) levels coupled with aberrant morphogenesis and chitin deposition in elm1Δ cells carrying ESCRT mutations suggest that ESCRTs normally enhance the efficiency of cell division by promoting timely endocytic turnover of key cytokinetic enzymes.