bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictive biomarkers and effectiveness of MUC1-targeted dendritic-cell-based vaccine in patients with refractory non-small cell lung cancer
Authors: Teramoto Koji , Ozaki Yoshitomo , Hanaoka Jun , Sawai Satoru , Tezuka Noriaki , Fujino Shozo , Daigo Yataro , Kontani Keiichi 
Published: November 2016

Background: The dendritic cell (DC)-based vaccine targeting the highly immunogenic tumor antigen, MUC1, has been promising for a cancer immunotherapy; however, predictive biomarkers for beneficial clinical responses of the vaccine remain to be determined. Methods: DCs loaded with MUC1-derived peptide were subcutaneously administered to patients with MUC1-positive non-small cell lung cancer (NSCLC) that was refractory to standard anticancer therapies, every 2 weeks. The effectiveness and tolerability of the vaccine were evaluated, and predictive biomarkers of clinical responses were explored. Results: Between August 2005 and May 2015, 40 patients received the vaccines. The median survival time (MST) after the initial vaccination was 7.4 months, and the 1-year survival rate was 25.0%. The MST for patients who received more than six vaccinations was 9.5 months, and the 1-year survival rate was 39.3%. In this cohort, patients who experienced immune-related adverse events, including skin reactions at the vaccination site and fever, had significantly longer survival times compared with patients without those immune-related adverse events (12.6 versus 6.7 months, p = 0.042). Longer survival times were also observed in patients whose peripheral white blood cells contained >20.0% lymphocytes (12.6 versus 4.5 months; p = 0.014). MUC1-specific cytotoxic immune responses were achieved in all of seven patients analyzed who received six vaccinations. Conclusion: The MUC1-targeted DC-based vaccine induced an antitumor immune response that promoted prolonged survival of patients with refractory NSCLC. The occurrence of immune-related adverse events and having a higher percentage of peripheral lymphocytes were predictive biomarkers of a beneficial clinical response during cancer immunotherapy for NSCLC.
Pokémon Go, the novelty of nostalgia, and the ubiquity of the smartphone
Authors: Keogh Brendan 
Published: November 2016

None of the elements that contribute to the phenomenon of Pokémon Go are particularly new. Augmented-reality and location-based games, artworks, and marketing campaigns have existed for well over a decade. Meanwhile, the Pokémon franchise of videogames, trading cards, comic books, and anime has existed for more than two. Even the data that Pokémon Go is built from is generated by players of Niantic’s earlier locative game, Ingress. If there is nothing “new” about the phenomenon of Pokémon Go, then what is there to learn from its rapid ascension in the cultural zeitgeist? In this article I maintain that it is the increased ubiquity of the smartphone and its tendency to reconfigure existing media and cultural practices that has allowed the novelty of augmented reality and the nostalgia of Pokémon to converge in a perfect storm of branding, design, preexisting data, and established technologies.
LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length
Authors: Bao Yu , Hayashida Morihiro , Akutsu Tatsuya 
Published: November 2016

Abstract
Background
Dicer is necessary for the process of mature microRNA (miRNA) formation because the Dicer enzyme cleaves pre-miRNA correctly to generate miRNA with correct seed regions. Nonetheless, the mechanism underlying the selection of a Dicer cleavage site is still not fully understood. To date, several studies have been conducted to solve this problem, for example, a recent discovery indicates that the loop/bulge structure plays a central role in the selection of Dicer cleavage sites. In accordance with this breakthrough, a support vector machine (SVM)-based method called PHDCleav was developed to predict Dicer cleavage sites which outperforms other methods based on random forest and naive Bayes. PHDCleav, however, tests only whether a position in the shift window belongs to a loop/bulge structure.

Result
In this paper, we used the length of loop/bulge structures (in addition to their presence or absence) to develop an improved method, LBSizeCleav, for predicting Dicer cleavage sites. To evaluate our method, we used 810 empirically validated sequences of human pre-miRNAs and performed fivefold cross-validation. In both 5p and 3p arms of pre-miRNAs, LBSizeCleav showed greater prediction accuracy than PHDCleav did. This result suggests that the length of loop/bulge structures is useful for prediction of Dicer cleavage sites.

Conclusion
We developed a novel algorithm for feature space mapping based on the length of a loop/bulge for predicting Dicer cleavage sites. The better performance of our method indicates the usefulness of the length of loop/bulge structures for such predictions.
MetaMIS: a metagenomic microbial interaction simulator based on microbial community profiles
Authors: Shaw Grace Tzun-Wen , Pao Yueh-Yang , Wang Daryi 
Published: November 2016

Abstract
Background
The complexity and dynamics of microbial communities are major factors in the ecology of a system. With the NGS technique, metagenomics data provides a new way to explore microbial interactions. Lotka-Volterra models, which have been widely used to infer animal interactions in dynamic systems, have recently been applied to the analysis of metagenomic data.

Results
In this paper, we present the Lotka-Volterra model based tool, the Metagenomic Microbial Interacticon Simulator (MetaMIS), which is designed to analyze the time series data of microbial community profiles. MetaMIS first infers underlying microbial interactions from abundance tables for operational taxonomic units (OTUs) and then interprets interaction networks using the Lotka-Volterra model. We also embed a Bray-Curtis dissimilarity method in MetaMIS in order to evaluate the similarity to biological reality. MetaMIS is designed to tolerate a high level of missing data, and can estimate interaction information without the influence of rare microbes. For each interaction network, MetaMIS systematically examines interaction patterns (such as mutualism or competition) and refines the biotic role within microbes. As a case study, we collect a human male fecal microbiome and show that Micrococcaceae, a relatively low abundance OTU, is highly connected with 13 dominant OTUs and seems to play a critical role. MetaMIS is able to organize multiple interaction networks into a consensus network for comparative studies; thus we as a case study have also identified a consensus interaction network between female and male fecal microbiomes.

Conclusions
MetaMIS provides an efficient and user-friendly platform that may reveal new insights into metagenomics data. MetaMIS is freely available at: https://sourceforge.net/projects/metamis/.
Early identification in primary health care of people at risk for sick leave due to work-related stress – study protocol of a randomized controlled trial (RCT)
Authors: Holmgren Kristina , Sandheimer Christine , Mårdby Ann-Charlotte , Larsson Maria E. H. , Bültmann Ute , Hange Dominique , Hensing Gunnel 
Published: November 2016

Abstract

Background
Early identification of persons at risk of sickness absence due to work-related stress is a crucial problem for society in general, and primary health care in particular. Tho date, no established method to do this exists. This project’s aim is to evaluate whether systematic early identification of work-related stress can prevent sickness absence. This paper presents the study design, procedure and outcome measurements, as well as allocation and baseline characteristics of the study population.

Method/design
The study is a two-armed randomized controlled trial with follow-up at 3, 6 and 12 months. Non-sick-listed employed women and men, aged 18 to 64 years, who had mental and physical health complaints and sought care at primary health care centers (PHCC) were eligible to participate. At baseline work-related stress was measured by the Work Stress Questionnaire (WSQ), combined with feedback at consultation, at PHCC. The preventive intervention included early identification of work-related stress by the WSQ, GP training in the use of WSQ, GP feedback at consultation and finding suitable preventive measures. A process evaluation was used to explore how to facilitate future implementation and structural use of the WSQ at the PHCC. The primary outcome to compare the preventive sick leave intervention by the general practitioner (GP) versus treatment as usual is sick leave data obtained from the Swedish Social Insurance Agency register.

Discussion
Early screening for sick leave due to work-related stress makes it possible not only to identify those at risk for sick leave, but also to put focus on the patient’s specific work-related stress problems, which can be helpful in finding suitable preventive measures. This study investigates if use of the WSQ by GPs at PHCCs, combined with feedback at consultation, prevents future sickness absence.

Trial registration
ClinicalTrials.gov. Identifier: NCT02480855. Registered 20 May 2015
A mixed-method study of the efficacy of physical activity consultation as an adjunct to standard smoking cessation treatment among male smokers in Malaysia
Authors: Lee Yuin Yi , Khoo Selina , Morris Tony , Hanlon Clare , Wee Lei-Hum , Teo Eng Wah , Adnan Yuhanis 
Published: November 2016

Abstract
Background
This study examined the effectiveness of using Physical Activity Consultation (PAC) as an addition to the standard smoking cessation treatment in Malaysia. We explored participants’ experiences in terms of physical activity and smoking abstinence with the combined PAC and smoking cessation intervention.

Methods
Walk-in smokers from a local smoking cessation clinic volunteered for the 8-week intervention program, while undergoing standard smoking cessation treatment. In Week 1, a facilitator conducted a face-to-face intervention to explore participants’ involvement in physical activity and helped to set physical activity strategies and goals for participants to increase physical activity levels. Participants were provided with follow-up phone calls at Weeks 3 and 6. Participants answered questionnaires that measured smoking withdrawal (Shiffman–Jarvik Withdrawal Scale), cessation self-efficacy (Cessation Self-efficacy Questionnaire), physical activity involvement (International Physical Activity Questionnaire), and mood (Brunel Mood Scale) upon recruitment, at post-intervention and at follow-up 3 months after the intervention ended. Participants also responded to interviews about their experiences with the PAC and smoking cessation treatment at post-intervention and at 3-month follow-up.

Results
Seven participants completed the program until follow-up. All were successfully abstinent. Only two participants increased physical activity levels, whereas others maintained their physical activity levels or showed slight decreases. Several themes were identified in this study, including participants’ experiences with withdrawal symptoms, smoking cessation self-efficacy, triggers to smoking cessation, thoughts on standard smoking cessation treatment in Malaysia, physical activity involvement, mood, and thoughts and beliefs on combining smoking cessation and physical activity.

Conclusions
This study suggests PAC was helpful in maintaining or increasing the overall physical activity levels of participants and could assist with smoking abstinence. Findings showed that all participants who stayed in the program were successfully abstinent. In general, the findings in this study provided promising results for further research on PAC as an adjunct to smoking cessation treatments in Malaysia.
Trial registration This intervention is registered with the Australian New Zealand Clinical Trials Registry (Trial registration number: ACTRN12616000269437).
Drosophila WASH is required for integrin-mediated cell adhesion, cell motility and lysosomal neutralization
Authors: Nagel Benedikt M. , Bechtold Meike , Rodriguez Luis Garcia , Bogdan Sven 
Published: November 2016

ABSTRACT
The Wiskott-Aldrich syndrome protein and SCAR homolog (WASH; also known as Washout in flies) is a conserved actin-nucleation-promoting factor controlling Arp2/3 complex activity in endosomal sorting and recycling. Previous studies have identified WASH as an essential regulator in Drosophila development. Here, we show that homozygous wash mutant flies are viable and fertile. We demonstrate that Drosophila WASH has conserved functions in integrin receptor recycling and lysosome neutralization. WASH generates actin patches on endosomes and lysosomes, thereby mediating both aforementioned functions. Consistently, loss of WASH function results in cell spreading and cell migration defects of macrophages, and an increased lysosomal acidification that affects efficient phagocytic and autophagic clearance. WASH physically interacts with the vacuolar (V)-ATPase subunit Vha55 that is crucial to establish and maintain lysosome acidification. As a consequence, starved flies that lack WASH function show a dramatic increase in acidic autolysosomes, causing a reduced lifespan. Thus, our data highlight a conserved role for WASH in the endocytic sorting and recycling of membrane proteins, such as integrins and the V-ATPase, that increase the likelihood of survival under nutrient deprivation.
Blood clotting behavior is innately modulated in Ursus Americanus during early and late denning relative to summer months
Authors: Iles Tinen L. , Laske Timothy G. , Garshelis David L. , Iaizzo Paul A. 
Published: November 2016

Remarkably, American black bears (Ursus Americanus) are capable of varying their heart rates to coincide with their breathing, creating pauses of 30 seconds or more, yet they do not appear to suffer from embolic events. We evaluated some features of the clotting cascade of black bears, providing novel insights on the underlying mechanisms they evoke for embolic protection during hibernation.
We measured activated clotting times, prothrombin times, and activated partial thromboplastin times during early-denning (December), late-denning (March), and summer (August). Activated clotting times during early hibernation were ∼3 times longer than those observed among non-hibernating animals. Clotting times declined later in hibernation, when bears were within ∼1 month of emerging from dens. Prothrombin times were similar for each seasonal time point, whereas activated partial thromboplastin times were highest during early-denning and decreased during late-denning and summer. We also examined D-dimer concentrations to assess whether the bears were likely to have experienced embolic events. None of the non-parturient bears exceeded a D-dimer concentration of 250 ng/mL (considered the clinical threshold for embolism in mammals).
Our findings suggest there is unique expression of the clotting cascade in American black bears during hibernation, in which extrinsic pathways are maintained but intrinsic pathways are suppressed. This was evaluated by a significant difference between the activated clotting times and activated partial thromboplastin times during the denning and non-denning periods. These changes are likely adaptive, to avoid clotting events during states of immobilization and/or periods of asystole. Yet, an intact extrinsic pathway allows for healing of external injuries and/or foreign body responses.
Gossypibomas, a surgeon's nightmare—patient demographics, risk factors, imaging and how we can prevent it
Authors: Mathew Rishi P , Thomas Binston , Basti Ram S , Suresh Hadihally B 
Published: November 2016

Objective:
Gossypibomas are a cottonoid matrix left behind following surgery. Owing to the legal issues associated with it, very few literature studies are available online, most of them being case reports. The purpose of our study was to identify the patient demographics, risk factors and imaging features.

Methods:
Six surgically identified and histopathologically confirmed cases of gossypibomas recorded over a period of 5 years from a single tertiary institution were retrospectively evaluated for patient demographics [sex, age, body mass index (BMI)], type of surgery and duration from time of surgery to onset of symptoms. Ultrasound and CT images obtained from our hospital database were evaluated for their characteristic pattern. Statistics used included percentage and frequency.

Results:
Females formed the bulk of our patients and the mean BMI of our patients was 24.25. The interval between surgery and symptom presentation ranged from 2 months to 7 years. The most common imaging patterns observed on ultrasound and CT were a thick-walled hypoechoic lesion with a strong posterior acoustic shadowing and a “spongiform pattern”, respectively.

Conclusion:
A detailed patient history, taking into account radiologist—surgeon interaction, along with familiarization of the various risk factors and imaging patterns can bring about an accurate diagnosis of a gossypiboma.

Advances in knowledge:
Our study showed that the female sex, especially those undergoing gynaecology-related surgery such as hysterectomy and patients with a high BMI were at risk of gossypibomas. The combination of a hypoechoic lesion with strong posterior shadowing on ultrasound along with a spongiform pattern on CT was highly characteristic for gossypiboma on imaging.
An end-of-life care nurse service for people with COPD and heart failure: stakeholders' experiences
Authors: Johnston Bridget , Coole Carolyn , Jay Narayanasamy Melanie 
Published: November 2016

Background: End-of-life care (EOLC) has historically been associated with cancer care. However, demographic changes indicate that future provision must also cater for other long term conditions (LTC). An EOLC-LTC service, delivered by palliative care nurses, is currently being piloted in one area in the East Midlands with patients with cardiac and respiratory disease. In order to inform future commissioning, it is important to gain the views and experiences of those involved with the service. Aims: This study aimed to explore patients, and their partners, views and experiences of the EOLC-LTC service. Methods: Semi-structured interviews were used as part of a case study design, involving six cases. Each case consisted of the patient, their nominated family member/carer and key healthcare professionals involved in their care as identified by the patient. This paper reports on the findings from the interviews conducted with the six patients and their family member/carers. Data were analysed thematically. Results: From the interviews, the following themes were identified: experiences managing a long term cardio-respiratory condition, the nurse service, building a close/therapeutic relationship and fragmentation and integration. Conclusions: This study has shown that the EOLC-LTC service is welcomed and highly regarded by patients and their family members/carers. Further studies are required to explore the views and experiences of other key stakeholders and to evaluate how well the pilot operates within the wider care pathway.
Moral justifications in the media debate on globalization in Finland, 1995–2014
Authors: Ylä-Anttila Tuomas 
Published: November 2016

AbstractThis article presents a methodological tool, Justifications Analysis, and uses it to analyze the debate on globalization in Finnish mass media between 1995 and 2014. Justifications Analysis focuses on the moral principles evoked to justify arguments, something that tends to be overlooked by most established approaches to media content analysis. Regarding the frequency of coverage, it is found that the debate in Finland deviates from the global issue attention cycle and lasts longer, driven by national key events. Concerning the groups of speakers, the Global Justice Movement is found to have initiated the debate; the elites are divided into two groups, one defending and the other opposing the movement. Moral justifications are used extensively. All parties to the debate justify their arguments by referring to the common good, but disagree over whether it should be defined in terms of market worth, equality and democracy, national values, or some combination of these.
Variation and relationships of morphological traits, shoot yields and essential oil contents of fourAnthemisspecies
Authors: Alizadeh Mohammad Ali , Jafari Ali Ashraf 
Published: November 2016

AbstractAnthemisL. is a genus of aromatic flowering plants in the family Asteraceae and is native to Iran. In this research, 62 accessions of four chamomile species includingAnthemis tinctoria, A. triumfetti, A. haussknechtiiandA. pseudocotulawere evaluated for morphological traits. Four experiments were conducted using a randomized complete block design with three replications at the Research Institute of Forest and Rangeland, Tehran, Iran in 2011. Data were collected for the morphological traits for all of the species and essential oil content forA. triumfettiandA. pseudocotula.The results showed that plant height was positively correlated with canopy area for all of the species exceptA. triumfetti(p< 0.01). There were positive correlations between flower number with plant height and canopy area in bothA. tinctoriaandA. haussknechtii(p< 0.01). Fresh and dry weight were positively correlated with canopy area and plant height in all of the species (p< 0.01), exceptA. tinctoriafor canopy area andA. triumfettifor plant height. GDD had a positive correlation with canopy area forA. triumfetti(p< 0.05). There was a positive correlation between essential oil yield and plant height, fresh and dry weight inA. triumfettiandA. pseudocotula(p< 0.05). Using cluster analysis (Ward method), the accessions ofA. triumfetti, A. tinctoria, A. haussknechtiiandA. pseudocotulawere grouped into 3, 2, 4 and 2 clusters, respectively. The results of cluster analysis separated the accession based on shoot yield, morphological traits and maturity. In some items, the accessions within each cluster were coordinated with their geographical provenance.
COST Action FP1105: effect of raw materials and pulping conditions on the characteristics of dissolved kraft lignins
Authors: Svärd Antonia , Sevastyanova Olena , Dobele Galina , Jurkjane Vilhemina , Brännvall Elisabet 
Published: November 2016

Abstract
The composition, molecular weight (MW), and chemical structure of technical lignins as byproducts of pulping influence their application in terms of physical and chemical properties, reactivity, and performance. It is important to know how the analytical data of technical lignins are influenced by the wood species and the parameters of pulping. The present study focuses on kraft pulping and how the wood species (eucalyptus, pine, and spruce) and variable cooking times influence the characteristics of dissolved lignins. The black liquor (BL) was recovered after three different cooking times and the precipitated lignin was characterized by total acid hydrolysis including the determination of the acid insoluble part (Klason lignin, KL) and the sugars in the hydrolysate, elemental analysis, 31P NMR spectroscopy, analytical pyrolysis (Py-GC/MS), gel permeation chromatography (GPC), thermogravimetry (TG), and differential scanning calorimetry (DSC). The results indicate that the phenolic OH content, MW and glass transition temperature increased with longer cooking times for the softwood (SW) lignins. These lignins had also a higher MW (Mw 5500–8000 g mol-1), than the eucalyptus lignin (Mw 2200–2400 g mol-1). Eucalyptus lignin had higher sulfur content compared to SW.