bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation of an Open Source Software solution for Laboratory Information Management and automated RNAseq data analysis in a large-scale Cancer Genomics initiative using BASE with extension package Reggie
Authors: Häkkinen Jari , Nordborg Nicklas , Månsson Olle , Vallon-Christersson Johan 
Published: February 2016

AbstractBackgroundLarge-scale cancer genomics initiatives and next-generation sequencing for transcriptome profiling allow for detailed molecular characterization of tumors, and provide opportunities for clinical tools to improve diagnosis, prognosis, and treatment decisions. Laboratory information, data management, and data sharing in large-scale genomics projects is a challenge. Aiming to introduce such technologies in a clinical setting offer additional challenges associated with requirements of short lead-times and specialized tracking of biomaterials, data, and analysis results.ResultsUsing the free open-source BioArray Software Environment (BASE) and extension package Reggie we have implemented a laboratory information management system and an automated RNAseq data analysis pipeline that successfully manage a large regional cancer genomics initiative. The system manages enrolled cancer patients, tumor biopsies, extraction of nucleic acid, and whole transcriptome RNA-sequencing through to data analysis and quality control. The implementation offers integration of laboratory equipment and operating procedures, and information tracking in a module based fashion enabling efficient and flexible use of personnel resources. The system provides two-factor authentication and transaction control and seamless integration of freely available software for RNAseq analysis such as Tophat, Cufflinks, and Picard. As of February 2016 more than 8000 patients and over 6000 tumor biopsies have been successfully processed. Lead-time from biopsy arrival to summarized reports based on RNAseq data is less than 5 days, in line with regional clinical requirements. BASE and Reggie are freely available and released as open-source under the GNU General Public License and GNU Affero General Public License, respectively.ConclusionUsing free open-source software together with BASE and a customized extension package, Reggie, we have implemented a system capable of managing large collections of quality controlled and curated material for use in research and development and tailored to meet requirements for clinical use. Featuring high degree of automation and interactivity the system allows for resource efficient laboratory procedures and short lead-times with demonstrated use of RNAseq data analyses in a clinical setting.
Convert Your Favorite Protein Modeling Program Into A Mutation Predictor: “MODICT”
Authors: Tanyalcin Ibrahim , Stouffs Katrien , Daneels Dorien , Al Assaf Carla , Lissens Willy , Jansen Anna , Gheldof Alexander 
Published: February 2016

AbstractMotivation:Predict whether a mutation is deleterious based on the custom 3D model of a protein.Methods:We have developed MGDIGT, a mutation prediction tool which isbased on per residuermsd(root mean square deviation) values of superimposed3D protein models. Our mathematical algorithm was tested for 42 describedmutations in multiple genes including renin, beta-tubulin, biotinidase,sphingomyelin phosphodiesterase-1, phenylalanine hydroxylase and medium chainAcyl-Coa dehydrogenase. Moreover,modictscores corresponded toexperimentally verified residual enzyme activities in mutated biotinidase,phenylalanine hydroxylase and medium chain Acyl-CoA dehydrogenase. Severalcommercially available prediction algorithms were tested and results werecompared. ThemodictPERL package and the manual can be downloaded fromhttps://github.com/MODICT/MODICT.Conclusion:We show here thatmodictis capable tool for mutation effectprediction at the protein level, using superimposed 3D protein models instead ofsequence based algorithms used by PGLYPHEN and SIFT.
Knowledge management in Mexican NPOs: a comparative study in organizations with a local and national presence
Authors: Zapata Cantu Laura E , Mondragon Carlota Eugenia 
Published: February 2016

Purpose– The purpose of this paper is to identify those organizational and personal elements that enable not-for-profit organizations (NPOs) to generate and transfer knowledge. NPOs are under pressure to use their financial and human resources efficiently, and to improve their activities and services constantly. Knowledge management as a strategy would ensure NPOs’ sustainability and rapid adaptation to dynamic environments.Design/methodology/approach– A qualitative study based on interviews, documents and questionnaires was conducted in 28 Mexican NPOs.Findings– Three main findings were identified: First, Mexican NPOs generate knowledge through courses and seminars based on volunteers’ personal motivation and organizational culture. Second, informal communication media are widely utilized to transfer organizational knowledge. Third, personal commitment to the organization’s mission and trust in their colleagues’ social actions are crucial for knowledge transfer effectiveness, rather than organizational elements.Research limitations/implications– Results scope of this study is limited to the NPOs under study. The findings expose some highlights for knowledge management process in NPOs in Mexico which would be tested in further research.Practical implications– Contrary to knowledge management in profit organizations, NPOs must recognize that personal motivation, commitment and trust in organization’s mission and social actions are crucial rather than organizational culture and top management support.Social implications– NPOs must convert their tacit knowledge to explicit knowledge, which allows NPOs to be transparent and effective, and to have access to more funding opportunities and to replicate their best practices throughout the organization.Originality/value– There are only few studies of knowledge management processes in NPOs. Some considerations have to be done with respect to personal motivation, commitment and trust, as well as organizational elements.
Barriers to knowledge sharing in third sector social care: a case study
Authors: Bloice Lyndsay , Burnett Simon 
Published: February 2016

Purpose
– This paper aims to build on existing theory of knowledge sharing barriers (KSBs) by exploring the concept in the relatively under-researched context of social service not-for-profit organisations.

Design/methodology/approach
– In this study, case study methodology was used. Practitioner staff members took part in online questionnaires, followed by semi-structured interviews with line management and middle management staff. Secondary sources from the case study organisation were also used in the analysis. The analysis of questionnaire responses alongside responses from semi-structured interviews is compared with extant research into KSBs.

Findings
– The findings of this study highlight the need to re-examine the KSBs identified in the literature to reflect contexts beyond the private sector. Common barriers were identified, but some found in the case study organisation did not neatly fit into the existing definitions of KSBs. An updated list of KSBs to reflect this social service not-for-profit context is presented.

Research limitations/implications
– Case studies are often not generalisable; however, the KSB list developed here could be further explored and tested in other third sector organisations.

Practical implications
– The research raises the question of applicability of current knowledge management (KM) theory and lexicon in the third sector and social care environment.

Originality/value
– This study provides an insight into KM applicability in a third sector context, which is a relatively under-developed research area.
Increase of interleukin‐10‐producing B cells associated with long‐term remission after i.v. immunoglobulin treatment for pemphigus
Authors: Kabuto Miho , Fujimoto Noriki , Tanaka Toshihiro 
Published: February 2016

AbstractWe present a refractory case of pemphigus vulgaris that achieved long‐term remission after i.v. immunoglobulin treatment (IVIG). We evaluated the fluctuation of circulating interleukin‐10‐producing B cells (B10 cells) during the course in our case and other three patients with pemphigus treated with IVIG without clinical remission. B10 cells were observed predominantly in CD1d–, CD5–, CD9– and CD27+ populations among CD19+ cells in healthy controls, as well as in patients with pemphigus. The frequency of B10 cells among CD19+ cells increased in our case, but not in the other three patients without clinical remission, which leads to speculation on the association between the increase of B10 cells and the achievement of long‐term remission after IVIG treatment.
Families dealing with the uncertainty of genetic disorders: the case of Neurofibromatosis Type 1
Authors: Carrieri Daniele , Farrimond Hannah , Kelly Susan , Turnpenny Peter 
Published: February 2016

AbstractSome scholars contend that genetic medicine is transforming the experience of illness and the social category of the family – bringing future risks into the present, and potentially strengthening familial biological bonds in light of these shared genetic risks. However, research has shown that genetic information is interpreted and acted upon through a rich repertoire of adaptable social, cultural and familial factors which pre‐exist and interact with biomedical knowledge. This paper reports research into families living with Neurofibromatosis Type 1 (NF1), a highly uncertain condition the manifestation of which can vary considerably also within the same family and, for this reason, has been defined as a ‘condition without parameters’. These characteristics makeNF1 a particularly informative condition for the examination of family dynamics around genetic information. The study and the methodology are based on the exploration of family networks and allow us to investigate the interrelation of individual and familial constructions of the uncertainty ofNF1. This also allows both theoretical and policy claims to be made about the danger of reductionist thinking about the transformative potential of genetic technologies.
Choosing a Nursing Home: What Do Consumers Want to Know, and Do Preferences Vary across Race/Ethnicity?
Authors: Hefele Jennifer Gaudet , Acevedo Andrea , Nsiah‐Jefferson Laurie , Bishop Christine , Abbas Yasmin , Damien Ecaterina , Ramos Candi 
Published: February 2016

ObjectiveTo identify what consumers want to know about nursing homes (NHs) before choosing one and to determine whether information preferences vary across race/ethnicity.Data Sources/Study SettingPrimary data were collected in Greater Boston (January 2013–February 2014) from community‐dwelling, white, black, and Latino adults aged 65+ and 40–64 years, who had personal/familial experience with a NH admission or concerns about one.Study DesignEleven focus groups and 30 interviews were conducted separately by race/ethnicity and age group.Principal FindingsParticipants wanted detailed information on the facility, policies, staff, and residents, such as location, staff treatment of residents, and resident conditions. They wanted a sense of the NH gestalt and were interested in feedback/reviews from residents/families. Black and Latino participants were especially interested in resident and staff racial/ethnic concordance and facility cultural sensitivity. Latino participants wanted information on staff and resident language concordance.ConclusionsConsumers want more information about NHs than what is currently available from resources like Nursing Home Compare. Report card makers can use these results to enhance their websites, and they should consider the distinct needs of different racial/ethnic groups. Future research should test methods for collecting and reporting resident and family feedback/reviews.
An Approach to Speaker Identification
Authors: Hollien Harry 
Published: February 2016

AbstractThis presentation will provide standards upon which any attempts to meet the challenge of identifying speakers by voice should be based. It is organized into a model based on (i) application of a rigorous research program validating the system, (ii) an upgrading of the organization of theSIarea, and (iii) exploitation of new technology. The second part of the presentation will describe an illustrative speech/voice approach toSIdevelopment. This effort is also based on an extensive corpus of research. It is suggested that application of the cited standards, plus the illustrative model, will permit reasonable progress to be made. Finally, a number of procedural recommendations are made; they should enhance the efficacy of the proposed approach.
Blood glucose screening among elderly Malaysians: Who to target?
Authors: Cheah Yong Kang , Goh Kim‐Leng 
Published: February 2016

AbstractBackgroundEarly detection of raised blood glucose can reduce the risk of developing diabetes. Despite being a high‐risk group, a significant proportion of the elderly population does not undergo blood glucose screening. The aim of the present study was to examine the factors affecting blood glucose screening among the elderly.MethodsData from a sample of 2463 respondents in the National Health and Morbidity Survey 2011 were used. Pearson Chi‐squared tests were conducted to find factors associated with screening behavior. A logit model was used to analyze the likelihood of screening.ResultsIncome, age, education, ethnicity, employment status, availability of medical coverage, and smoking behavior were significantly associated with blood glucose screening. The likelihood of blood glucose screening was positively correlated with available monthly income and was higher in those aged 60–69 years, those attaining higher education, Malays, and elderly who are medically covered.ConclusionsThe findings of the present study provide insights for health policy formulation for the elderly. As part of their efforts to reduce national health costs, governments should pay particular attention to the elderly, who are likely to be unscreened for blood glucose levels, because they face even larger risk exposure.
Is internal jugular vein extensibility associated with indices of fluid responsiveness in ventilated patients?
Authors: Thudium M. , Klaschik S. , Ellerkmann R. K. , Putensen C. , Hilbert T. 
Published: February 2016

BackgroundUltrasound of the inferior vena cava provides rapid and non‐invasive assessment of fluid responsiveness. We hypothesized that the extensibility of the internal jugular vein (IJV) as well reflects intravascular volume state. We assessedIJVdimensions together with pulse pressure variation (PPV) as dynamic index for fluid responsiveness in mechanically ventilated patients.MethodsOf 50 patients after cardiac surgery were assessed. Ultrasound ofIJVdimensions as well as collection of hemodynamic data were performed in 30° and horizontal (0°) position, and the ventilator‐ and position‐inducedIJVextensibilities (E‐IJV) were calculated.ResultsMean ventilator‐induced E‐IJVin 30° position was 56%, and meanPPVin 30° position was 13.7%. Changing the patient's position from 30° to 0° significantly reduced ventilator‐induced E‐IJVas well asPPV. Pearson's correlation test revealed significant association between ventilator‐induced E‐IJVand fluid responsiveness deduced fromPPVin 0° position (r= 0.43,P< 0.005). An E‐IJVthreshold >5% identified patients with significantly elevatedPPVvalues.ConclusionUltrasound of theIJVandPPVas a dynamic index for fluid responsiveness can be associated under certain defined conditions. Whether or not ultrasound of theIJVcan be useful to predict patient intravascular volume state should be further studied using invasive cardiac output monitoring.
Habitat selection in a reintroduced population: social effects differ between natal and post‐release dispersal
Authors: Richardson K. M. , Ewen J. G. 
Published: February 2016

AbstractUnderstanding the factors driving dispersal behaviour and habitat selection in reintroduced populations can be critical to reintroduction success. Social factors in particular can influence habitat selection, for example through conspecific attraction, and this can have both positive and negative effects on reintroduction success, particularly where multiple releases occur. In addition, little is known about how habitat selection differs between natal and post‐release dispersal within species. Often it is assumed that information from a species’ natal dispersal preferences and patterns can act as a guide for predicting post‐release dispersal behaviour, but no studies to date have examined this. We examine the factors influencing habitat selection during both natal and post‐release dispersal in a reintroduced hihi (stitchbird, Notiomystis cincta) population using species distribution models. We demonstrate a strong social effect in habitat selection of natal dispersers bred at the release area (largely the offspring of founders), yet find no social effect in habitat selection of juveniles translocated 2 years after the first releases occurred. In addition, we establish that environmental variables are important in habitat selection in both groups. We suggest (1) that consideration of social effects and conspecific attraction should play a role in planning reintroduction release strategies, especially if reinforcement releases are considered necessary, and (2) that it may not always be appropriate to assume post‐release dispersal in reintroduced populations will be driven by the same factors that influence natal dispersal.
Pooled population pharmacokinetic model of imipenem in plasma and the lung epithelial lining fluid
Authors: van Hasselt J. G. Coen , Rizk Matthew L. , Lala Mallika , Chavez‐Eng Cynthia , Visser Sandra A. G. , Kerbusch Thomas , Danhof Meindert , Rao Gauri , van der Graaf Piet H. 
Published: February 2016

AimsSeveral clinical trials have confirmed the therapeutic benefit of imipenem for treatment of lung infections. There is however no knowledge of the penetration of imipenem into the lung epithelial lining fluid (ELF), the site of action relevant for lung infections. Furthermore, although the plasma pharmacokinetics (PK) of imipenem has been widely studied, most studies have been based on selected patient groups. The aim of this analysis was to characterize imipenem plasma PK across populations and to quantify imipenem ELF penetration.MethodsA population model for imipenem plasma PK was developed using data obtained from healthy volunteers, elderly subjects and subjects with renal impairment, in order to identify predictors for inter‐individual variability (IIV) of imipenem PK. Subsequently, a clinical study which measured plasma and ELF concentrations of imipenem was included in order to quantify lung penetration.ResultsA two compartmental model best described the plasma PK of imipenem. Creatinine clearance and body weight were included as subject characteristics predictive for IIV on clearance. Typical estimates for clearance, central and peripheral volume, and inter‐compartmental clearance were 11.5 l h–1, 9.37 l, 6.41 l, 13.7 l h–1, respectively (relative standard error (RSE) <8%). The distribution of imipenem into ELF was described using a time‐independent penetration coefficient of 0.44 (RSE 14%).ConclusionThe identified lung penetration coefficient confirms the clinical relevance of imipenem for treatment of lung infections, while the population PK model provided insights into predictors of IIV for imipenem PK and may be of relevance to support dose optimization in various subject groups.
Nutraceuticals with a clinically detectable blood pressure‐lowering effect: a review of available randomized clinical trials and their meta‐analyses
Authors: Borghi Claudio , Cicero Arrigo F G 
Published: February 2016

AIMSThe aim of the present study was to review and comment on the available evidence on nutraceuticals with a clinically demonstrable blood pressure (BP)‐lowering effect.METHODSWe reviewed studies published in the English language from 1990 to 2015 on dietary supplements or nutraceuticals claiming to show an effect on human BP. An initial list of possibly effective agents and studies was obtained from the online reference, the Natural Medicine Comprehensive Database. Using PubMed, we searched agents identified from this list using the MeSH terms ‘hypertension’, ‘blood pressure’, ‘dietary supplement’ and ‘nutraceuticals’, alone and in combination. We then focused our attention on meta‐analyses and randomized clinical trials.RESULTSBeyond the well‐known effects on BP of the Dietary Approaches to Stop Hypertension (DASH) and the Mediterranean diet, a large number of studies have investigated the possible BP‐lowering effect of different dietary supplements and nutraceuticals, most of which are antioxidant agents with a high tolerability and safety profile. In particular, a relatively large body of evidence supports the use of potassium, magnesium, L‐arginine, vitamin C, cocoa flavonoids, beetroot juice, coenzyme Q10, controlled‐release melatonin and aged garlic extract. The antihypertensive effect of all these nutraceuticals seems to be dose related and the overall tolerability is good.CONCLUSIONSome nutraceuticals might have a positive impact on BP in humans. Further clinical research is needed, to identify from the available active nutraceuticals those with the best cost‐effectiveness and risk–benefit ratio for widespread and long‐term use in the general population with a low‐added cardiovascular risk related to uncomplicated hypertension.
Long‐term outcome of insulin pump therapy: reduction of hypoglycaemia and impact on glycaemic control
Authors: Quirós C. , Giménez M. , Ríos P. , Careaga M. , Roca D. , Vidal M. , Conget I. 
Published: February 2016

AbstractAimsTo determine the long‐term outcome of continuous subcutaneous insulin infusion (CSII) in Type 1 diabetes according to Catalan National Health Service indications.MethodsRetrospective observational study including 178 patients with Type 1 diabetes who started CSII treatment in our centre (2003–2008). All patients were followed in our CSII programme for outpatients for at least 5 years. Data on annual HbA1c levels were collected, and the main indication for starting CSII was analysed.ResultsTwenty‐seven of 178 patients were excluded because of loss to follow‐up or withdrawal from CSII, thus 151 patients (aged 37.4 ± 10.5 years, 64% women) were analysed. The main indications for starting CSII were suboptimal metabolic control (60.9%), severe hypoglycaemia/hypoglycaemia unawareness (25.5%) and others (13.6%). HbA1c was 64 ± 13 mmol/mol (8.0 ± 1.2%) at the start of CSII and 62 ± 13 mmol/mol (7.8 ± 1.2%) after 5 years in the total cohort (P = 0.1). The severe hypoglycaemia rates were 0.66 ± 1.61 and 0.17 ± 0.42 episodes/patient/year (P < 0.001). In patients with suboptimal metabolic control, HbA1c decreased from 68 ± 12 mmol/mol (8.4 ± 1.1%) to 64 ± 14 mmol/mol (8.0 ± 1.3%) (P = 0.016), with 37.4% of those in this group having an HbA1c ≤ 58 mmol/mol (7.5%) after 5 years. In patients starting CSII due to severe hypoglycaemia the problem was considered resolved in 93%, and in 64% of those starting CSII because of suboptimal glycaemic control, HbA1c improved significantly.ConclusionsCSII therapy achieves and maintains its efficacy mainly in terms of reducing severe hypoglycaemia. In the whole group of patients, the reduction in HbA1c is transient and disappears after 5 years.