bluuebunny/crossref_metadata_2025_split huggingface dataset:
Living With Chronic Obstructive Pulmonary Disease
Authors: Chen Kang-Hua , Liu Chien-Ying , Shyu Yea-Ing Lotus , Yeh Shu-Ling 
Published: March 2016

ABSTRACT

Background:
Disease self-management for patients with chronic obstructive pulmonary disease (COPD) is less well characterized than that for patients with other chronic diseases. A patient-centered perspective calls for qualitative research to investigate the process of self-management as a means of enhancing quality of life in patients with COPD.

Purpose:
This study explores the process of self-management for patients with COPD and the factors that impact the efficacy of this process.

Methods:
A qualitative inquiry approach was used to collect data in the thoracic ward, outpatient department, and respiratory therapy room of a medical center in Taiwan. A convenience sample of 19 patients was collected. Qualitative content analysis was used to analyze data.

Results:
Living with COPD is a process that involves self-regulation and selecting suitable healthcare behaviors. The related healthcare behaviors identified in this study include symptom management, exercise implementation, environmental control, emotional adjustment, maintenance of a healthy life style, and utilization of community and healthcare resources. The factors that were found to influence this process include the physical and psychological conditions of the patient, his or her disease-related cognition, and the social support that he or she receives. In this study, once participants became dissatisfied with the consequences of their healthcare behaviors, they chose a new set of healthcare behaviors and continued to engage in the process of self-regulation.

Conclusions/Implications for Practice:
Patients naturally become experts with regard to their lives through a process of trial and error. Even so, healthcare professionals play a key role in the process of self-management and help patients with COPD cope with various problems in their daily lives. The findingsof this study contribute to the development of evidence-based self-management interventions that promote quality of life in patients with COPD.
Increased prevalence of heparin-induced thrombocytopenia in patients with Budd–Chiari syndrome: a retrospective analysis
Authors: Zaman Sameer , Wiebe Stefan , Bernal William , Wendon Julia , Czuprynska Julia , Auzinger Georg 
Published: March 2016

Background
Budd–Chiari syndrome (BCS) is a rare, potentially fatal disease characterized by hepatic venous outflow tract obstruction. Heparin-induced thrombocytopenia (HIT) is an immune-mediated complication of heparin therapy, with mortality approaching 10%. The reported prevalence of HIT in adults is 0.2–5.2%. Expert consensus through case reports is the only existing evidence of HIT in BCS. To our knowledge, this is the first study to formalize this anecdotal evidence.

Methods
A retrospective analysis was carried out of patients presenting at a tertiary liver centre with acute liver failure because of BCS or BCS as the primary indication for liver transplantation between 2000 and 2013. The prevalence of HIT in the study group was compared with the highest reported prevalence in adult medical patients receiving heparin (5.2%). Mortality, length of stay and liver transplantation rates were also studied.

Results
Of 32 BCS patients, 9 (28.1%) developed HIT, significantly higher than the previously reported prevalence of HIT in medical patients (5.2%) (P<0.0001). There was no difference in mortality (P=0.66), length of stay (P=0.58) and liver transplantation rate (P=0.39) between HIT-positive and HIT-negative patients.

Conclusion
The prevalence of HIT (28.1%) in our cohort of BCS patients is significantly higher than that in the general population (0.2–5.2%). Although this study was not powered to detect outcome differences, as heparin is the mainstay of acute BCS treatment, this represents a significant risk. We recommend a high index of suspicion for HIT in patients with BCS and thrombocytopenia, an appropriate HIT-testing strategy and consideration of direct thrombin inhibitors.
Combination of Vascular Intervention Surgery and Free Tissue Transfer for Critical Diabetic Limb Salvage
Authors: Chou Chieh , Kuo Pao-Jen , Chen Yen-Chou , Huang Shu-Hung , Chang Chih-Hau , Wu Yi-Chia , Lee Su-Shin , Lai Cheng-Sheng , Lin Sin-Daw , Chang Kao-Ping , Kuo Yur-Ren 
Published: March 2016

Background
Complex, nontraumatic diabetic foot ulcers with peripheral vascular compromise often lead to extensive lower-limb amputation. The aim of this study is to determine the outcome of combined vascular intervention and free tissue transfer for critical diabetic limb salvage.

Materials and Methods
A total of 26 consecutive diabetic patients with 28 legs with diabetic foot ulcers who underwent limb salvage with a combination of revascularization (bypass surgery or endovascular angioplasty) and free flap transfers were reviewed. There were 14 male and 12 female patients. The average age was 58.8 years (range, 35–85 years). Amputation-free survival and complete wound healing were defined as the primary endpoints. All preoperative and postoperative data were retrospectively analyzed.

Results
Thirty flaps were used for reconstruction in 28 legs, including 21 free anterolateral thigh (ALT) perforator flaps, 3 ALT myocutaneous flaps, 5 gracilis muscle flaps, and 1 latissimus dorsi muscle flap. All flaps used end-to-side anastomoses for the recipient artery and end-to-end anastomoses for the recipient vein. The overall flap success rate was 90% (27/30). Two flaps failed completely because of severe arteriosclerosis, which resulted in anastomosed vessel thrombosis. New flaps were applied in both cases after debridement and trimming of necrotic tissue. One flap failed because of restenosis and inadequate perfusion combined with severe infection, resulting in pedicle thrombosis. A below-knee amputation was subsequently performed. Seven flaps exhibited a partial loss, including 6 ALT perforator flaps and 1 latissimus dorsi flap, because of inadequate margin perfusion. After debridement, the flap revision and wound care, 5 flaps healed uneventfully without additional intervention. The remaining 2 ALT perforator flaps required debridement with a skin graft. The limb-salvage rates were 92.8% after 1 year and 89.2% after 5 years.

Conclusions
The combination of peripheral arterial intervention and free tissue transfer resulted in successful wound healing and limb salvage instead of amputation in select diabetic patients with difficult-to-heal wounds.
testCryopreservation of human mucosal leukocytes
Authors: Hughes Sean M. , Shu Zhiquan , Levy Claire N. , Ferre April L. , Hartig Heather , Fang Cifeng , Lentz Gretchen , Fialkow Michael , Kirby Anna C. , Adams Waldorf Kristina M. , Veazey Ronald S , Germann Anja , Briesen Hagen von , McElrath M. Juliana , Dezzutti Charlene S. , Sinclair Elizabeth , Baker Chris A. R. , Shacklett Barbara L , Gao Dayong , Hladik Florian 
Published: March 2016

AbstractBackgroundUnderstanding how leukocytes in the cervicovaginal and colorectal mucosae respond to pathogens, and how medical interventions affect these responses, is important for developing better tools to prevent HIV and other sexually transmitted infections. An effective cryopreservation protocol for these cells following their isolation will make studying them more feasible.Methods and findingsTo find an optimal cryopreservation protocol for mucosal mononuclear leukocytes, we compared cryopreservation media and procedures using human vaginal leukocytes and confirmed our results with endocervical and colorectal leukocytes. Specifically, we measured the recovery of viable vaginal T cells and macrophages after cryopreservation with different cryopreservation media and handling procedures. We found several cryopreservation media that led to recoveries above 75%. Limiting the number and volume of washes increased the fraction of cells recovered by 10-15%, possibly due to the small cell numbers in mucosal samples. We confirmed that our cryopreservation protocol also works well for both endocervical and colorectal leukocytes.Cryopreserved leukocytes had slightly increased cytokine responses to antigenic stimulation relative to the same cells tested fresh. Additionally, we tested whether it is better to cryopreserve endocervical cells on the cytobrush or in suspension.ConclusionsLeukocytes from cervicovaginal and colorectal tissues can be cryopreserved with good recovery of functional, viable cells using several different cryopreservation media. The number and volume of washes has an experimentally meaningful effect on the percentage of cells recovered. We provide a detailed, step-by-step protocol with best practices for cryopreservation of mucosal leukocytes.
Complete mitochondrial genome ofMuricea crassaandMuricea purpurea(Anthozoa: Octocorallia) from the eastern tropical Pacific
Authors: Poliseno Angelo , Breedy Odalisca , Eitel Michael , Wöerheide Gert , Guzman Hector M. , Krebs Stefan , Blum Helmuth , Vargas Sergio 
Published: March 2016

AbstractWe sequenced the complete mitogenomes of two eastern tropical Pacific gorgonians,Muricea crassaandMuricea purpurea,using NGS technologies. The assembled mitogenomes ofM. crassaandM. purpureawere 19,586 bp and 19,358 bp in length, with a GC-content ranging from 36.0% to 36.1%, respectively. The two mitogenomes had the same gene arrangement consisting of 14 protein-coding genes, two rRNAs and one tRNA. Mitogenome identity was 98.5%. The intergenic regions betweenCOBandNAD6and betweenNAD5andNAD4were polymorphic in length with a high level of nucleotide diversity. Based on a concatenated dataset of 14 mitochondrial protein-coding genes we inferred the phylogeny of 26 octocoral species.
Forward genetics by sequencing EMS variation induced inbred lines
Authors: Addo-Quaye Charles , Buescher Elizabeth , Best Norman , Chaikam Vijay , Baxter Ivan , Dilkes Brian P. 
Published: March 2016

ABSTRACTIn order to leverage novel sequencing techniques for cloning genes in eukaryotic organisms with complex genomes, the false positive rate of variant discovery must be controlled for by experimental design and informatics. We sequenced five lines from three pedigrees of EMS mutagenized Sorghum bicolor, including a pedigree segregating a recessive dwarf mutant. Comparing the sequences of the lines, we were able to identify and eliminate error prone positions. One genomic region contained EMS mutant alleles in dwarfs that were homozygous reference sequence in wild-type siblings and heterozygous in segregating families. This region contained a single non-synonymous change that cosegregated with dwarfism in a validation population and caused a premature stop codon in the sorghum ortholog encoding the giberellic acid biosynthetic enzyme ent-kaurene oxidase. Application of exogenous giberillic acid rescued the mutant phenotype. Our method for mapping did not require outcrossing and introduced no segregation variance. This enables work when line crossing is complicated by life history, permitting gene discovery outside of genetic models.This inverts the historical approach of first using recombination to define a locus and then sequencing genes. Our formally identical approach first sequences all the genes and then seeks co-segregation with the trait. Mutagenized lines lacking obvious phenotypic alterations are available for an extention of this approach: mapping with a known marker set in a line that is phenotypically identical to starting material for EMS mutant generation.
Assessing the measurement transfer function of single-cell RNA sequencing
Authors: Dueck Hannah R. , Ai Rizi , Camarena Adrian , Ding Bo , Dominguez Reymundo , Evgrafov Oleg V. , Fan Jian-Bing , Fisher Stephen A. , Hernstein Jennifer S. , Kim Tae Kyung , Kim Jae Mun (Hugo) , Lin Ming-Yi , Liu Rui , Mack William J. , McGroty Sean , Nguyen Joseph , Salathia Neeraj , Shallcross Jamie , Souaiaia Tade , Spaethling Jennifer , Walker Chris P. , Wang Jinhui , Wang Kai , Wang Wei , Wilberg Andre , Zheng Lina , Chow Robert H. , Eberwine James , Knowles James A. , Zhang Kun , Kim Junhyoung 
Published: March 2016

AbstractRecently, measurement of RNA at single cell resolution has yielded surprising insights. Methods for single-cell RNA sequencing (scRNA-seq) have received considerable attention, but the broad reliability of single cell methods and the factors governing their performance are still poorly known. Here, we conducted a large-scale control experiment to assess the transfer function of three scRNA-seq methods and factors modulating the function. All three methods detected greater than 70% of the expected number of genes and had a 50% probability of detecting genes with abundance greater than 2 to 4 molecules. Despite the small number of molecules, sequencing depth significantly affected gene detection. While biases in detection and quantification were qualitatively similar across methods, the degree of bias differed, consistent with differences in molecular protocol. Measurement reliability increased with expression level for all methods and we conservatively estimate the measurement transfer functions to be linear above ~5-10 molecules. Based on these extensive control studies, we propose that RNA-seq of single cells has come of age, yielding quantitative biological information.
The power and pitfalls of Dirichlet-multinomial mixture models for ecological count data
Authors: O’Brien John D. , Record Nicholas R. , Countway Peter 
Published: March 2016

AbstractThe Dirichlet-multinomial mixture model (DMM) and its extensions provide powerful new tools for interpreting the ecological dynamics underlying taxon abundance data. However, like many complex models, how effectively they capture the many features of empirical data is not well understood. In this work, we expand the DMM to an infinite mixture model (iDMM) and use posterior predictive distributions (PPDs) to explore the performance in three case studies, including two amplicon metagenomic time series. We avoid concentrating on fluctuations within individual taxa and instead focus on consortial-level dynamics, using straight-forward methods for visualizing this perspective. In each study, the iDMM appears to perform well in organizing the data as a framework for biological interpretation. Using the PPDs, we also observe several exceptions where the data appear to significantly depart from the model in ways that give useful ecological insight. We summarize the conclusions as a set of considerations for field researchers: problems with samples and taxa; relevant scales of ecological fluctuation; additional niches as outgroups; and possible violations of niche neutrality.
Mechanical signals inhibit growth of a grafted tumorin vivo: Proof of Concept
Authors: Brossel Rémy , Yahi Alexandre , David Stéphane , Moreno Velasquez Laura , Guinebretière Jean-Marc 
Published: March 2016

ABSTRACTIn the past ten years, many studies have shown that malignant tissue has been “normalized”in vitrousing mechanical signals. We apply the principles of physical oncology (or mechanobiology)in vivoto show the effect of a “constraint field” on tumor growth. The human breast cancer cell line, MDA MB 231, admixed with ferric nanoparticles was grafted subcutaneously in Nude mice. The magnetizable particles rapidly surrounded the growing tumor. Two permanent magnets located on either side of the tumor created a gradient of magnetic field. Magnetic energy is transformed into mechanical energy by the particles acting as “bioactuators”, applying a constraint field and, by consequence, biomechanical stress to the tumor. This biomechanical treatment was applied 2 hours/day during 21 days, from Day 18 to Day 39 following tumor implantation. The study lasted 74 days. Palpable tumor was measured two times a week. There was a significantin vivodifference between the median volume of treated tumors and untreated controls in the mice measured up to D 74 (D 59 + population): (529 [346; 966] mm3vs 1334 [256; 2106] mm3; p=0.015), treated mice having smaller tumors. The difference was not statistically significant in the group of mice measured at least to D 59 (D 59 population). Onex vivoexamination, the surface of the tumor mass, measured on histologic sections, was less in the treated group, G1, than in the control groups: G2 (nanoparticles, no magnetic field), G3 (magnetic field, no nanoparticles), G4 (no nanoparticles, no magnetic field) in the D 59 population (Median left surface was significantly lower in G1 (5.6 [3.0; 42.4] mm2, p=0.005) than in G2 (20.8 [4.9; 34.3]), G3 (16.5 [13.2; 23.2]) and G4 (14.8 [1.8; 55.5]); Median right surface was significantly lower in G1 (4.7 [1.9; 29.2] mm2, p=0.015) than in G2 (25.0 [5.2; 55.0]), G3 (18.0 [14.6; 35.2]) and G4 (12.5 [1.5; 51.8]). There was no statistically significant difference in the day 59+ population. This is the first demonstration of the effect of stress on tumor growthin vivosuggesting that biomechanical intervention may have a high translational potential as a therapy in locally advanced tumors like pancreatic cancer or primary hepatic carcinoma for which no effective therapy is currently available.
Hormetic Shifting of Redox Environment by Pro-Oxidative Resveratrol Protects Cells Against Stress
Authors: Plauth Annabell , Geikowski Anne , Cichon Susanne , Wowro Silvia J. , Liedgens Linda , Rousseau Morten , Weidner Christopher , Fuhr Luise , Kliem Magdalena , Jenkins Gail , Lotito Silvina , Wainwright Linda J. , Sauer Sascha 
Published: March 2016

AbstractResveratrol has gained tremendous interest owing to multiple reported health-beneficial effects. However, the underlying key mechanism of action of resveratrol remained largely controversial. Here, we demonstrate that under physiologically relevant conditions major biological effects of resveratrol can be attributed to the generation of oxidation products such as reactive oxygen species (ROS). At low hormetic concentrations (< 50 μM), treatment with resveratrol increased cell viability in a set of representative cell models, whereas application of quenchers of ROS completely truncated these beneficial effects. Notably, application of resveratrol led to mild, Nrf2-specific cellular gene expression reprogramming. For example, in primary human epidermal keratinocytes this resulted in a 1.3-fold increase of endogenous metabolites such as gluthathione (GSH) and subsequently in a quantitative reduction of the cellular redox environment by 2.61 mV mmol GSH (g protein)-1. In particular in resveratrol pre-treated cells, after external application of oxidative stress by using 0.8 % ethanol, endogenous ROS generation was consequently reduced by 24 %. In contrast to the common perception that resveratrol acts mainly as a chemical antioxidant or as a target protein-specific ligand, we propose that effects from resveratrol treatment are essentially based on oxidative triggering of cells. In relevant physiological microenvironments this effect can lead to hormetic shifting of cellular defence towards a more reductive state to improve resilience to oxidative stress in a manner that can be exactly defined by the redox-environment of the cell.
Mapping and Inheritance analysis of a novel dominant rice male sterility mutant,OsDMS-1
Authors: Yang Kun , Chen Yun , Shi Min , Converse Richard , Chen Xin , Min Hengqi , Zhao Baimei , Zhang Yi , Lv Jun 
Published: March 2016

AbstractWe found a rice dominant genetic male sterile mutantOsDMS-1from the tissue culture regenerated offspring of Zhonghua 11 (japonicarice). Compared to wild Zhonghua 11,OsDMS-1mutant anthers were thinner and whiter, and could not release any pollen although the glume opened normally; most of the mutant pollen was small and malformed, and could not be stained by iodine treatment; a paraffin section assay showed the degradation ofOsDMS-1mutant tapetum was delayed, with no accumulation of starch in the mutant pollen, ultimately leading to pollen abortion. Classical genetic analysis indicated that only one dominant gene was controlling the sterility in theOsDMS-1mutant. However, molecular mapping suggested three loci simultaneously control male sterility in this mutant:OsDMS-1A,flanked by InDel markers C1D4 and C1D5 with a genetic distance of 0.15 and 0.30 cM, respectively;OsDMS-1B,flanked by InDel markers C2D3 and C2D10 with a genetic distance of 0.44 and 0.88 cM, respectively;OsDMS-1C,flanked by InDel markers 0315 and C3D3 with a genetic distance of 0.44 and 0.88 cM, respectively. Molecular mapping disagreed with classical genetic analysis about the number of controlling genes in theOsDMS-1mutant, indicating a novel mechanism underlying sterility inOsDMS-1. We present two hypotheses to explain this novel inheritance behavior: one is described as Parent-Originated Loci Tying Inheritance (POLTI); or the hypothesis is described as Loci Recombination Lethal (LRL).Key messageThree loci, which were localized on the chromosomes 1, 2 and 3 respectively, simultaneously control a dominant rice male sterility in this mutant:OsDMS-1.
A Multidisciplinary Approach to Explain Biological Aging and Longevity
Authors: Augsburger Brett N. 
Published: March 2016

AbstractScientists have been unable to reach a consensus on why organisms age and why they live as long as they do. Here, a multidisciplinary approach was taken in an attempt to understand the root causes of aging. Nonequilibrium thermodynamics may play a previously unappreciated role in determining longevity by governing the dynamics of degradation and renewal within biomolecular ensembles and dictating the inevitability of fidelity loss. The proposed model offers explanations for species longevity trends that have been previously unexplained and for aging-related observations that are considered paradoxical within current paradigms—for example, the elevated damage levels found even in youth within many long-lived species, such as the naked mole-rat. This framework questions whether declining selective pressure is the primary driver of aging, and challenges major tenets of the disposable soma theory. Unifying pertinent principles from diverse disciplines leads to a theoretical framework of biological aging with fewer anomalies, and may be useful in predicting outcomes of experimental attempts to modulate the aging phenotype.