bluuebunny/crossref_metadata_2025_split huggingface dataset:
ADEPT, a dynamic next generation sequencing data error-detection program with trimming
Authors: Feng Shihai , Lo Chien-Chi , Li Po-E , Chain Patrick S. G. 
Published: February 2016

Abstract
Background
Illumina is the most widely used next generation sequencing technology and produces millions of short reads that contain errors. These sequencing errors constitute a major problem in applications such as de novo genome assembly, metagenomics analysis and single nucleotide polymorphism discovery.

Results
In this study, we present ADEPT, a dynamic error detection method, based on the quality scores of each nucleotide and its neighboring nucleotides, together with their positions within the read and compares this to the position-specific quality score distribution of all bases within the sequencing run. This method greatly improves upon other available methods in terms of the true positive rate of error discovery without affecting the false positive rate, particularly within the middle of reads.

Conclusions
ADEPT is the only tool to date that dynamically assesses errors within reads by comparing position-specific and neighboring base quality scores with the distribution of quality scores for the dataset being analyzed. The result is a method that is less prone to position-dependent under-prediction, which is one of the most prominent issues in error prediction. The outcome is that ADEPT improves upon prior efforts in identifying true errors, primarily within the middle of reads, while reducing the false positive rate.
To develop a regional ICU mortality prediction model during the first 24 h of ICU admission utilizing MODS and NEMS with six other independent variables from the Critical Care Information System (CCIS) Ontario, Canada
Authors: Kao Raymond , Priestap Fran , Donner Allan 
Published: February 2016

Abstract
Background
Intensive care unit (ICU) scoring systems or prediction models evolved to meet the desire of clinical and administrative leaders to assess the quality of care provided by their ICUs. The Critical Care Information System (CCIS) is province-wide data information for all Ontario, Canada level 3 and level 2 ICUs collected for this purpose. With the dataset, we developed a multivariable logistic regression ICU mortality prediction model during the first 24 h of ICU admission utilizing the explanatory variables including the two validated scores, Multiple Organs Dysfunctional Score (MODS) and Nine Equivalents Nursing Manpower Use Score (NEMS) followed by the variables age, sex, readmission to the ICU during the same hospital stay, admission diagnosis, source of admission, and the modified Charlson Co-morbidity Index (CCI) collected through the hospital health records.

Methods
This study is a single-center retrospective cohort review of 8822 records from the Critical Care Trauma Centre (CCTC) and Medical-Surgical Intensive Care Unit (MSICU) of London Health Sciences Centre (LHSC), Ontario, Canada between 1 Jan 2009 to 30 Nov 2012. Multivariable logistic regression on training dataset (n = 4321) was used to develop the model and validate by bootstrapping method on the testing dataset (n = 4501). Discrimination, calibration, and overall model performance were also assessed.

Results
The predictors significantly associated with ICU mortality included: age (p < 0.001), source of admission (p < 0.0001), ICU admitting diagnosis (p < 0.0001), MODS (p < 0.0001), and NEMS (p < 0.0001). The variables sex and modified CCI were not significantly associated with ICU mortality. The training dataset for the developed model has good discriminating ability between patients with high risk and those with low risk of mortality (c-statistic 0.787). The Hosmer and Lemeshow goodness-of-fit test has a strong correlation between the observed and expected ICU mortality (χ2 = 5.48; p > 0.31). The overall optimism of the estimation between the training and testing data set ΔAUC = 0.003, indicating a stable prediction model.

Conclusions
This study demonstrates that CCIS data available after the first 24 h of ICU admission at LHSC can be used to create a robust mortality prediction model with acceptable fit statistic and internal validity for valid benchmarking and monitoring ICU performance.
Genome sequences of Knoxdaviesia capensis and K. proteae (Fungi: Ascomycota) from Protea trees in South Africa
Authors: Aylward Janneke , Steenkamp Emma T. , Dreyer Léanne L. , Roets Francois , Wingfield Brenda D. , Wingfield Michael J. 
Published: February 2016

AbstractTwo closely related ophiostomatoid fungi, Knoxdaviesia capensis and K. proteae, inhabit the fruiting structures of certain Protea species indigenous to southern Africa. Although K. capensis occurs in several Protea hosts, K. proteae is confined to P. repens. In this study, the genomes of K. capensis CBS139037 and K. proteae CBS140089 are determined. The genome of K. capensis consists of 35,537,816 bp assembled into 29 scaffolds and 7940 predicted protein-coding genes of which 6192 (77.98 %) could be functionally classified. K. proteae has a similar genome size of 35,489,142 bp that is comprised of 133 scaffolds. A total of 8173 protein-coding genes were predicted for K. proteae and 6093 (74.55 %) of these have functional annotations. The GC-content of both genomes is 52.8 %.
Methods of conducting a service audit at the regional level
Authors: Платонова Наталья , Platonova Natalya , Вапнярская Ольга , Vapnyarskaya Olga 
Published: February 2016

This article continues the series of publications of authors, in which they presented a description of the conceptual
basis of auditing service, its methodological foundations, recommendations for the standardization and separate
objects and processes. The article presents the description of a new approach to the application of the concept and
methodology service audit. Previously the audit service was viewed solely as a method of monitoring the adequacy, service quality and its conformity with the needs of the target consumer groups, designed for individual enterprises
and their associations. Developing the service audit issues, the authors propose opportunities in research at the mesolevel
(at the regional level). Methodology service audit was used in the project to study service within the boundaries
of one of the tourist destinations in Russia. The difference is in the fact that the method of service audits, including
secret shopper method, was applied to a diverse set of objects constituting the regional tourism infrastructure. This
methodological tool was the same for all objects, which required a determination common to a variety of enterprises of
the conditions and elements of service of tourists. This approach allowed creating a unified database of the obtained
primary information, and later conducting a comparative study. The article presents some results of using the service
audit methods, data and conclusions regarding the completeness and quality of the tourism service destination,
obtained with its help. The results of the service audit of the regional tourism infrastructure describe the quality of
service in such elements of the tourist infrastructure, as hotels and other accommodation facilities, catering facilities,
objects and means of entertainment, objects of cognitive, business, medical, sports and other purposes. The authors
also presented a brief description of the methodology of used approach. Experience showed that such a project has all
the advantages of using the method of mystery shopping, including relatively low cost, the shortening of studies, etc.
the Conclusions resulting from the project were of interest to investors and regional tourism administrations.
‘I will keep and character that name’: Dramatis Personae Lists in Early Modern Manuscript Plays
Authors: Pangallo Matteo A. 
Published: February 2016

<p>W.W. Greg’s claim that manuscript plays containing character lists were intended for publication (print or manuscript) and not playhouse use fails to account for all of the evidence in surviving manuscripts. Instead, as this essay demonstrates, a more significant variable in the inclusion of character lists in manuscript plays is the writer’s professional or amateur status. This article argues that amateur playwrights, influenced by their experiences as readers of printed plays, were more likely than professionals to include the 'readerly' device of a dramatis personae list in their manuscript plays, even in the case of playhouse manuscripts.</p><p> </p><p><span><br /></span></p>
Search for Information on Multiple Products
Authors: Ke T. Tony , Shen Zuo-Jun Max , Villas-Boas J. Miguel 
Published: February 2016

We develop a framework for continuous search for information on a choice set of multiple alternatives and apply it to consumer search in a product market. When a consumer considers purchasing a product in a product category, the consumer can gather information sequentially on several products. At each moment, the consumer can choose which product to gather more information on and whether to stop gathering information and purchase one of the products or to exit the market with no purchase. Given costly information gathering, consumers end up not gathering complete information on all the products and need to make decisions under imperfect information. Under the assumption of constant informativeness of search, we solve for the optimal search, switch, and purchase or exit behavior in such a setting, which is characterized by an optimal consideration set and a purchase threshold structure. This paper shows that a product is only considered for search or purchase if it has a sufficiently high expected utility. Given multiple products in the consumer’s consideration set, the consumer only stops searching for information and purchases a product if the difference between the expected utilities of the top two products is greater than some threshold. Comparative statics show that negative information correlation among products widens the purchase threshold, and so does an increase in the number of the choices. Under our rational consumer model, we show that choice overload can occur when consumers search or evaluate multiple alternatives before making a purchase decision. We also find that it is optimal for a monopolistic seller of multiple products to facilitate information search for low-valuation consumers and obfuscate information for those with high valuations.This paper was accepted by Eric Anderson, marketing.
Person–Organization Fit and Incentives: A Causal Test
Authors: Andersson Ola , Huysentruyt Marieke , Miettinen Topi , Stephan Ute 
Published: February 2016

We investigate the effects of organizational culture and personal values on performance under individual and team contest incentives. We develop a model of regard for others and in-group favoritism that predicts interaction effects between organizational values and personal values in contest games. These predictions are tested in a computerized lab experiment with exogenous control of both organizational values and incentives. In line with our theoretical model, we find that prosocial (proself)-orientated subjects exert more (less) effort in team contests in the primed prosocial organizational values condition, relative to the neutrally primed baseline condition. Further, when the prosocial organizational values are combined with individual contest incentives, prosocial subjects no longer outperform their proself counterparts. These findings provide, to our knowledge, a first, affirmative, causal test of person–organization fit theory. They also suggest the importance of a “triple-fit” between personal preferences, organizational values, and incentive mechanisms for prosocially orientated individuals. This paper was accepted by John List, behavioral economics.
Can Contracts Signal Social Norms? Experimental Evidence
Authors: Danilov Anastasia , Sliwka Dirk 
Published: February 2016

We investigate whether incentive schemes signal social norms and thus affect behavior beyond their direct economic consequences. A one-shot principal–agent experiment is studied where prior to contract choice principals are informed about the past actions of other agents and thus have more information about norms of behavior. Compared with a setting in which principals are uninformed, agents exert substantially higher effort under a fixed wage contract when they are aware that an informed principal chose this contract. The informed principal’s choice apparently signals a norm not to exploit trust, which leads to more trustworthy behavior. This mechanism’s robustness is explored in further experiments. Data, as supplemental material, are available at http://dx.doi.org/10.1287/mnsc.2015.2336 . This paper was accepted by Uri Gneezy, behavioral economics.
The Disciplinary Effects of Proxy Contests
Authors: Fos Vyacheslav 
Published: February 2016

Using a manually collected data set of all proxy contests from 1994 through 2012, I show that proxy contests play an important role in hostile corporate governance. Target shareholders benefit from proxy contests: the average abnormal returns reach 6.5% around proxy contest announcements. Proxy contests that address firms’ business strategies and undervaluation are most beneficial for shareholders. By contrast, proxy contests that aim at changing capital structure and governance do not lead to higher firm values. Relative to matching firms, future targets are smaller, they have higher stock liquidity, higher institutional and activist ownership, lower leverage and market valuation, and higher investments. Whereas most of these characteristics predict proxy contests in time series, prior to proxy contests, targets also experience poor stock performance, decreases in investments, increases in cash reserves and payouts to shareholders, and increases in management’s entrenchment. These changes in corporate policies are consistent with targets’ attempts to affect the probability of a proxy contest. This paper was accepted by Amit Seru, finance.
Formal Enforcement Actions and Bank Behavior
Authors: Delis Manthos D. , Staikouras Panagiotis K. , Tsoumas Chris 
Published: February 2016

Employing a unique data set for the period 2000–2010, this paper examines the impact of formal enforcement actions targeting the core of the banks’ financial safety and soundness in terms of bank capital, risk, and performance. We find that, on average, these actions reduce both the risk-weighted assets and the nonperforming loans ratios of punished banks, but there is no increase in the level of regulatory capital. These effects are less powerful during the postcrisis period, suggesting that banks’ scope to improve their safety and soundness condition in crisis periods is much more limited. We also find, albeit with some limitations, that the timing of formal enforcement actions is important: the more the actions are deferred relative to the continuous deterioration of the banks’ financial condition, the more limited their impact on the risk-based capital ratio, while actions taken earlier help banks to improve their financial soundness. Data, as supplemental material, are available at http://dx.doi.org/10.1287/mnsc.2015.2343 . This paper was accepted by Wei Jiang, finance.
Short break and emergency respite care: what options for young people with life-limiting conditions?
Authors: Mitchell Tracy K , Knighting Katherine , O'Brien Mary R , Jack Barbara A 
Published: February 2016

Background: Service providers face difficult decisions about how best to develop services for the increasing numbers of young people with life-limiting conditions who require palliative care. Objective: To explore alternative short break and emergency respite care options to children's hospice care. Methods: A two-phase evaluation with young people, families and professionals. Phase 1: qualitative semi-structured interviews and focus groups (n=53). Phase 2: mixed-method survey (n=82), qualitative findings only. Results: There were few, or no, appropriate short break and emergency respite care alternatives when children's hospice care was not available that can meet the need of young people with life-limiting conditions, creating anxiety for children's hospice users and those leaving the service as a result of reaching transition age or through no longer meeting the children's hospice eligibility criteria. Conclusion: Access to appropriate short break and emergency respite care is required to prevent lifelong negative consequences for young people with life-limiting conditions, their family and society. Research is undoubtedly required to explore the impact and outcomes of children's hospice discharge for young people and their family. Particular attention should be paid to the lack of services for an increasing population making the transition from children's hospices.
Circumstances surrounding deaths from the perspective of bereaved Honduran families
Authors: Stone Arianna , LaMotta Cara P , Baudino Marissa N , Akard Terrah Foster , Gilmer Mary Jo 
Published: February 2016

Purpose: This qualitative study examined how bereaved individuals from Honduras responded to deaths of loved ones, particularly through exploring circumstances surrounding deaths and various coping strategies. Methods: With the help of a translator, bereaved family members in Honduras were interviewed using a semi-structured format. The interactions were audio-recorded and later translated and transcribed. Results: Some 60% of individuals spent time with other family members during their loved one's end of life and 22.5% of grieving individuals took solace in spirituality or religious practices and connecting with God. Some 40% wanted to speak with others through support groups. When individuals spoke about remembering the deceased, both comforting and discomforting effects were expressed. Conclusions: Further research is needed to learn more about coping strategies in various cultures and support mechanisms that health professionals can use or suggest when working with bereaved individuals.
Evaluating a pilot paediatric hospice-at-home service: a literature review
Authors: Hillis Rowan , Ling Julie , Quinn Claire , Brenner Maria 
Published: February 2016

Background: This literature review aims to offer practitioners an overview of the key components involved in designing the evaluation of a paediatric hospice-at-home pilot that will assess the effectiveness, efficiency and sustainability of the programme. The literature was reviewed in two stages: the first examined existing literature in the area of paediatric palliative care. The second looked at the wider field of adult palliative care to gain further insights into evaluation tool design. The findings are presented as a conceptual model to highlight each component of the pilot development stage as identified for evaluation purposes, emphasising their role and impact on the resultant delivery of integrated care. The clarity and transparency of this model offers a comprehensive overview of the evaluation process to all involved in the pilot.
Chaperone use amongst UK urological surgeons – an evaluation of current practice and opinion
Authors: Modgil V , Barratt R , Summerton DJ , Muneer A 
Published: February 2016

Introduction Intimate examinations are routinely performed by urologists as part of clinical practice. To protect patients and doctors, the General Medical Council offers guidance on the use of chaperones for intimate examinations. We assessed the opinions and use of chaperones amongst members of the British Association of Urological Surgeons (BAUS). Methods An online questionnaire comprising 12 questions on the use of chaperones in clinical practice was sent to all full, trainee and speciality doctor members of BAUS. Results The questionnaire had a response rate of 26% (n=331). The majority of respondents were consultant urologists, comprising 78.8% (n=261), with a wide range of years of experience. Of the respondents, 38.9% were not aware of the GMC guidance on chaperones. While 72.5% always used a chaperone., 22.9% never use a chaperone when the patient was of the same sex. Chaperones were most commonly used for intimate examinations (64.6%), and for examinations involving members of the opposite sex (77.3%). A majority of respondents felt that chaperones protect both the patient (77.3%), and the doctor (96.6%). However, 42.5% did not feel that using a chaperone assists the doctor’s examination, and some (17.2%) participants felt that chaperones were unnecessary. Conclusions This study shows considerable variability amongst urologists in their use of chaperones. A significant proportion of respondents were not aware of the GMC guidelines and did not regularly use a chaperone during an intimate examination. In addition, practice appears to be gender biased. Further study and education is suggested.
Effectiveness of a care bundle to reduce surgical site infections in patients having open colorectal surgery
Authors: Tanner J , Kiernan M , Hilliam R , Davey S , Collins E , Wood T , Ball J , Leaper D 
Published: February 2016

Introduction In 2010 a care bundle was introduced by the Department of Health (DH) to reduce surgical site infections (SSIs) in England. To date, use of the care bundle has not been evaluated despite incorporating interventions with resource implications. The aim of this study was to evaluate the DH SSI care bundle in open colorectal surgery. Methods A prospective cohort design was used at two teaching hospitals in England. The baseline group consisted of 127 consecutive patients having colorectal surgery during a 6-month period while the intervention group comprised 166 patients in the subsequent 6 months. SSI and care bundle compliance data were collected using dedicated surveillance staff. Results Just under a quarter (24%) of the patients in the baseline group developed a SSI compared with just over a quarter (28%) in the care bundle group (p>0.05). However, compliance rates with individual interventions, both before and after the implementation of the bundle, were similar. Interestingly, in only 19% of cases was there compliance with the total care bundle. The single intervention that showed an associated reduction in SSI was preoperative warming (p=0.032). Conclusions The DH care bundle did not reduce SSIs after open colorectal surgery. Despite this, it is not possible to state that the bundle is ineffective as compliance rates before and after bundle implementation were similar. All studies evaluating the effectiveness of care bundles must include data for compliance with interventions both before and after implementation of the care bundle; poor compliance may be one of the reasons for the lower than expected reduction of SSIs.