bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generation of sequence-based data for pedigree-segregating Mendelian or Complex traits
Authors: Li Biao , Wang Gao T. , Leal Suzanne M. 
Published: July 2015

Abstract
Motivation: There is great interest in analyzing next generation sequence data that has been generated for pedigrees. However, unlike for population-based data there are only a limited number of rare variant methods to analyze pedigree data. One limitation is the ability to evaluate type I and II errors for family-based methods, due to lack of software that can simulate realistic sequence data for pedigrees.
Summary: We developed RarePedSim (Rare-variant Pedigree-based Simulator), a program to simulate region/gene-level genotype and phenotype data for complex and Mendelian traits for any given pedigree structure. Using a genetic model, sequence variant data can be generated either conditionally or unconditionally on pedigree members’ qualitative or quantitative phenotypes. Additionally, qualitative or quantitative traits can be generated conditional on variant data. Sequence data can either be simulated using realistic population demographic models or obtained from sequence-based studies. Variant sites can be annotated with positions, allele frequencies and functionality. For rare variants, RarePedSim is the only program that can efficiently generate both genotypes and phenotypes, regardless of pedigree structure. Data generated by RarePedSim are in standard Linkage file (.ped) and Variant Call (.vcf) formats, ready to be used for a variety of purposes, including evaluation of type I error and power, for association methods including mixed models and linkage analysis methods.
Availability and Implementation: bioinformatics.org/simped/rare
Contact: sleal@bcm.edu
Association of Intraoperative Hypotension with Acute Kidney Injury after Elective Noncardiac Surgery
Authors: Sun Louise Y. , Wijeysundera Duminda N. , Tait Gordon A. , Beattie W. Scott 
Published: July 2015

AbstractAbstract
In a retrospective study of 5,127 patients undergoing noncardiac surgery, an increased risk of postoperative acute kidney injury (defined as >50% or 0.3 mg/dl increase in serum creatinine concentration) was found when intraoperative mean arterial pressure was less than 60 mmHg for more than 20 min and less than 55 mmHg for more than 10 min.
Supplemental Digital Content is available in the text.

Background:
Intraoperative hypotension (IOH) may be associated with postoperative acute kidney injury (AKI), but the duration of hypotension for triggering harm is unclear. The authors investigated the association between varying periods of IOH with mean arterial pressure (MAP) less than 55, less than 60, and less than 65 mmHg with AKI.

Methods:
The authors conducted a retrospective cohort study of 5,127 patients undergoing noncardiac surgery (2009 to 2012) with invasive MAP monitoring and length of stay of 1 or more days. Exclusion criteria were preoperative MAP less than 65 mmHg, dialysis dependence, urologic surgery, and surgical duration less than 30 min. The primary exposure was IOH. The primary outcome was AKI (50% or 0.3 mg/dl increase in creatinine) during the first 2 postoperative days. Multivariable logistic regression was used to model the exposure–outcome relationship.

Results:
AKI occurred in 324 (6.3%) patients and was associated with MAP less than 60 mmHg for 11 to 20 min and MAP less than 55 mmHg for more than 10 min in a graded fashion. The adjusted odds ratio of AKI for MAP less than 55 mmHg was 2.34 (1.35 to 4.05) for 11- to 20-min exposure and 3.53 (1.51 to 8.25) for more than 20 min. For MAP less than 60 mmHg, the adjusted odds ratio for AKI was 1.84 (1.11 to 3.06) for 11- to 20-min exposure.

Conclusions:
In this analysis, postoperative AKI is associated with sustained intraoperative periods of MAP less than 55 and less than 60 mmHg. This study provides an impetus for clinical trials to determine whether interventions that promptly treat IOH and are tailored to individual patient physiology could help reduce the risk of AKI.
Propensity Score Adjusted Comparison of MIDCAB versus Full Sternotomy Left Anterior Descending Artery Revascularization
Authors: Raja Shahzad G. , Benedetto Umberto , Alkizwini Eman , Gupta Sapna , Amrani Mohamed 
Published: July 2015

Objective Minimally invasive direct coronary artery bypass (MIDCAB) has been proposed as an attractive alternative to full sternotomy (FS) revascularization in isolated left anterior descending (LAD) artery disease not suitable for percutaneous coronary intervention. However, surgeons are still reluctant to perform MIDCAB owing to concerns about early and late outcomes. We aimed to compare short- and long-term outcomes after MIDCAB versus FS revascularization. Methods Prospectively collected data from institutional database were reviewed. Data for late mortality were obtained from the General Register Office. MIDCAB was performed in 318 patients, whereas 159 had FS, according to the surgeon's preference, among 477 patients with isolated LAD disease. Inverse propensity score weighting was used to estimate treatment effects on short- and long-term outcomes. Results In the propensity score-adjusted analysis, FS revascularization versus MIDCAB was associated increased rate of surgical site infection [4 (2.8%) versus 1 (0.7%); P = 0.04]. The 2 groups did not significantly differ with regard to other complications including operative mortality. Mean length of hospital stay was similar for the 2 groups. After a mean follow-up time of 6.2 years (interquartile range, 3.5–9.7 years), compared to MIDCAB, FS was not associated with an improved late survival (β coef, −1.42; standard error, 1.65; P = 0.39) or risk reduction for repeat revascularization (β coef, 1.22; standard error, 1.41; P = 0.15). Conclusions MIDCAB was associated with a trend toward better short-term outcomes and excellent long-term results comparable to FS revascularization. According to these findings, surgeons should not be reluctant to perform MIDCAB in isolated LAD disease.
In Vitro Hemocompatibility Testing of Dyneema Purity Fibers in Blood Contact
Authors: Basir Amir , de Groot Philip , Gründeman Paul F. , Tersteeg Claudia , Maas Coen , Barendrecht Arjan , Van Herwaarden Joost , Kluin Jolanda , Moll Frans , Pasterkamp Gerard , Roest Mark 
Published: July 2015

Objective Heart valve and vascular prosthesis implantation is a common procedure for patients with heart valve stenosis or regurgitation and dilated or obstructive vascular disease. Drawbacks of conventional valve prostheses are the requirement for anticoagulant drugs, moderate durability, and suboptimal resistance to fatigue and tear. Dyneema Purity fibers are made from ultra-high-molecular-weight polyethylene filaments and are very thin, flexible, and fatigue and abrasion resistant and have high strength. Therefore, prostheses made from Dyneema Purity fibers might be attractive for use in the minimally invasive treatment of valvular- and vascular diseases. The aim of this study was to test the hemocompatibility of Dyneema Purity fibers in contact with blood. Methods Real-time platelet adhesion in human blood of 3 volunteers was quantified after 5 minutes of perfusion on single filaments (Ø 15 μm) of Dyneema Purity and polyester fibers. Plasma thrombin generation was measured by fluoroscopy for patches of Dyneema Purity fibers and for 5 commonly used polyester and expanded polytetrafluoroethylene cardiovascular prostheses. Results Platelet adhesion per 1 mm was 6 ± 1.4 on Dyneema Purity filaments and 15 ± 3.4 on polyester filaments ( P = 0.02). Total formed thrombin and the time to peak of its maximum were noninferior for patches of Dyneema Purity fibers compared with the reference materials. Conclusions Dyneema Purity fibers are noninferior in adhesion and coagulation activation compared with commonly used cardiovascular prostheses.
Thoracoscopic Occlusion of the Left Atrial Appendage
Authors: Mokracek Ales , Kurfirst Vojtech , Bulava Alan , Hanis Jiri , Tesarik Richard , Pesl Ladislav 
Published: July 2015

Objective Left atrial appendage (LAA) plays a crucial role in the etiopathogenesis and the prevention of the stroke in patients with nonvalvular atrial fibrillation (AF). This paper presents our first experience with thoracoscopic LAA occlusion using an external clip. Methods We performed a total of 30 LAA occlusions with the AtriClip from left thoracoscopy approach during the period from July 2012 to July 2013. AtriClip was implanted during the bilateral thoracoscopic radiofrequency (RF) as part of left atrial ablation procedure. Results Among the 30 procedures, AtriClip was once periprocedurally partially positioned. In the remaining procedures, the implantation was successful without complications. Of the 30 patients, 29 underwent transesophageal echocardiography and computer tomography examination at 3 months after the procedure. Apart from the patient with the partial clip placement, a residual pouch of 18 mm was detected in another patient. In the remaining group (28/30 patients, 93%), the exclusion was complete. No migration or any other clip implantation-related complications occurred during the follow-up. None of the patients experienced an embolization event. Conclusions Endoscopic AtriClip implantation appears to be a reproducible and safe method of LAA occlusion, with a minimal risk and a high efficiency. In our opinion, the AtriClip implantation is a reasonable part of thoracoscopic AF treatment and should be considered as an alternative tool for stroke risk reduction in patients with AF.
The Surgical Treatment of Toxic Megacolon in Hirschsprung Disease
Authors: Khasanov Rasul , Schaible Thomas , Wessel Lucas M. , Hagl Cornelia Irene 
Published: July 2015

Objectives
Enterocolitis remains the most significant cause of morbidity and mortality in Hirschsprung disease (HD). It could progress into toxic megacolon (TM)—acute dilatation of the colon as accompanying toxic complication of Hirschsprung enterocolitis. It is a devastating complication, especially in infants with so far undiagnosed HD.

Methods
A retrospective analysis of medical records of 4 infants with TM was performed. The diagnosis TM was determined on the basis of clinical information (abdominal pain or tenderness, abdominal distension, diarrhea, bloody diarrhea, and constipation), plain x-rays of the abdomen (segmental or total colonic dilation), and the presence of such criteria (fever, high heart rate, increased white blood cell count, C reactive protein, anemia, dehydration, electrolyte disturbances, hypotension). Surgical management and outcome was evaluated by retrospective chart review.

Results
The median duration of symptoms characteristic for TM was 3 days. Toxic megacolon was seen as the first manifestation of previously unknown HD in 3 patients; in 1 newborn, the contrast radiograph was suggestive of HD. In all patients, conservative treatment was failed. Three patients were treated with surgical decompression and ileostomy only. In all these cases, severe complications occurred, consequently 2 of them died. In 1 patient, a resection of the transverse dilated colon additionally was performed. This patient had no complications in postoperative period and survived.

Conclusions
Because of the high mortality in patients with TM that were treated medically or with colonic decompression, a resection of massively distended part of the colon should be performed.
Inference of super-exponential human population growth via efficient computation of the site frequency spectrum for generalized models
Authors: Gao Feng , Keinan Alon 
Published: July 2015

AbstractThe site frequency spectrum (SFS) and other genetic summary statistics are at the heart of many population genetics studies. Previous studies have shown that human populations had undergone a recent epoch of fast growth in effective population size. These studies assumed that growth is exponential, and the ensuing models leave unexplained excess amount of extremely rare variants. This suggests that human populations might have experienced a recent growth with speed faster than exponential. Recent studies have introduced a generalized growth model where the growth speed can be faster or slower than exponential. However, only simulation approaches were available for obtaining summary statistics under such models. In this study, we provide expressions to accurately and efficiently evaluate the SFS and other summary statistics under generalized models, which we further implement in a publicly available software. Investigating the power to infer deviation of growth from being exponential, we observed that decent sample sizes facilitate accurate inference, e.g. a sample of 3000 individuals with the amount of data expected from exome sequencing allows observing and accurately estimating growth with speed deviating by 10% or more from that of exponential. Applying our inference framework to data from the NHLBI Exome Sequencing Project, we found that a model with a generalized growth epoch fits the observed SFS significantly better than the equivalent model with exponential growth (p-value = 3.85 × 10−6). The estimated growth speed significantly deviates from exponential (p-value << 10−12), with the best-fit estimate being of growth speed 12% faster than exponential.
Innovative behaviour in the workplace
Authors: Wojtczuk-Turek Agnieszka , Turek Dariusz 
Published: July 2015

Purpose– The purpose of this paper is to describe and explain the manner in which HR system’s flexibility, in combination with employees’ individual flexibility (IF) and their positive character traits, such as: optimism, hope, resistance or self-efficacy (which comprise psychological capital (PsychCap)), allow to predict employees’ readiness to display innovative behaviors in the workplace.Design/methodology/approach– A quantitative research methodology was adopted which resulted in the development of a both self-administered online survey instrument (n=166) and employees students in the postgraduate program at the Warsaw School of Economics (n=70). Using a national database of service companies, a random sample of 700 e-mail addresses was generated and respondents were invited to participate in the online survey. This resulted in the completion of 166 online surveys, representing a response rate of 26 percent. The second group of respondents consisted of 70 employees from different organizations in Poland.Findings– On the basis of the analyses it was shown that HR flexibility (HRF) and IF are a generally weak predictor of innovative behaviors. However, in a situation when PsychCap is set to be a mediator, these variables allow to predict innovative work behavior.Originality/value– Research on the relation of HRF to innovative behaviors has not been sufficiently clarified so far. The achieved results shed new light on the relations of these two variables and indicate that HRF does not translate directly into behaviors of the personnel. However, it should be noted that the relationship of these variables are of indirect nature.
Selecting ideas for new product development
Authors: Cui Geng , Peng Ling , Florès Laurent Pierre 
Published: July 2015

Purpose
– New product concept screening, i.e., selecting a few viable innovative concepts from numerous candidates, involves high stakes and is complicated and resource intensive. Over the years, there has been heated debate about the relative merit of monadic (sequential) tests vs that of preference-based paired comparisons. The paper aims to discuss these issues.

Design/methodology/approach
– This study proposes the Generalizability Theory as a framework to assess and compare the performance of traditional monadic test with the Adaptive Concept Screening (ACS) in terms of their testing results and psychometric quality.

Findings
– Using 50 yogurt concepts and two independent groups of respondents, the results indicate that ACS requires a significant smaller sample of respondents to achieve a necessary minimum G coefficient for decision making. Moreover, ACS offers a more discriminating and reliable solution for early stage concept screening as manifested by a higher G coefficient and greater percentage of variance due to the selected concepts given the same sampling design.

Practical implications
– The results lend strong support to ACS as a more cost-effective method for screening new product concepts and the Generalizability Theory as a systematic framework for assessing concept testing methods.

Originality/value
– This study adopts the Generalizability Theory framework to assess the validity of new product concept screening method.
Bridge and redundant ties in networks: the impact on innovation in food SMEs
Authors: Shiri Ghasem , Sauvée Loïc , Abdirahman Zam-Zam 
Published: July 2015

Purpose– The purpose of this paper is to study the impact of networks diversity on innovation activity of firms. It aims to review the structural issue in innovation networks and to distinguish different structures of networks for product and process innovation through an empirical research.Design/methodology/approach– Using a data set of 348 European agri-food firms, the authors study the impact of bridge and redundant ties on product and process innovation of firms. This is an empirical research based on an online survey in five European countries.Findings– The finding shows that bridge ties (measured by the number of heterogeneous networks in which firm participate) always facilitate product innovation in firms. The authors found also that a high number of heterogeneous ties in term of partners (simultaneous presence of redundant and non-redundant ties) motivate both product and process innovation in firms. Furthermore, the authors found a positive impact of network competence on process innovation.Research limitations/implications– The measures of bridge ties and redundant ties are indirect measures. This choice is a willing choice. Direct measurement of bridge and redundant ties always requires in-depth interviews with firms managers and thereby are limited by the number of observations.Originality/value– Research on innovations networks are dominated by case studies and researches with limited number of observations. Studying the networking behaviour, particularly the tie selection, of a wide range of firms brings additional knowledge in this field of research.
The outset of U-I R & D relationships: the specific case of biological sciences
Authors: Pinheiro Miguel Linhares , Pinho José Carlos , Lucas Cândida 
Published: July 2015

Purpose– The purpose of this paper is to draw insights from the actors-resources-activities (ARA) model and social capital literature to identify relevant activities shared by university-industry (U-I) actors prior to R & D cooperation.Design/methodology/approach– Based on a qualitative methodology, a series of interviews were carried out with researchers from the biological sciences domain.Findings– This study found that, at the outset of U-I links, companies’ motivations are strongly organizational, while academics are motivated at a personal level. The interactions grow from low-risk activities to partnerships on complex tasks, and depend on relational resources framed within the ARA and social capital theories. Results showed that shared interests are present at the outset of U-I links and grow thereafter. Trust and commitment were not ubiquitous at the outset, but rather at later stages of the cooperation, as a result of the developed interdependencies.Research limitations/implications– The combination of the ARA model and social capital in U-I links highlighted the different relationship levels (individual vs organizational), the disparities between early and established ties, and the interplay between low- and high-investment activities underlying researchers’ relationships. Several managerial contributions are presented for universities to promote greater integration with industry partners.Originality/value– A new direction of research is presented towards lower levels of U-I cooperation, taking into account the relational resources and the activities shared in each level. This work distinguished the different actors’ motivations and clarified the role of trust and commitment at the outset of U-I links. This first assessment of Portuguese U-I interactions within the biological sciences provided valuable insights for both academics and practitioners.
The influence of research and development policy: the case of Estonia in the EU
Authors: Reiljan Janno , Paltser Ingra 
Published: July 2015

Purpose
– The purpose of this paper is to evaluate the international position of Estonia among the member states of the EU and countries closely associated with the EU, from the perspective of the effect of research and development (R
&
D) policy on innovation activities in the business sector.

Design/methodology/approach
– Based on existing scientific research literature on the relationships between R
&
D policy and business sector R
&
D activities and innovation performance, a set of indicators describing R
&
D policy measures was created for the business sector. Using principal component analysis (PCA) method, independent robust dimensions of R
&
D policy were brought out. After eliminating the problem of multicollinearity in R
&
D policy indicators, robust multiple regression models were conducted to present a comprehensive empirical description of the shaping of business sector R
&
D and innovation activities in the sample of investigated countries.

Findings
– Based on the literature, the influences of R
&
D policy measures on business sector R
&
D activities and innovation performance were systemised; public R
&
D policy dimensions were empirically defined; the intensity of R
&
D policy influence on business sector R
&
D activities was estimated; the differences between real and prognostic values of business sector performance indicators in Estonia were calculated in order to characterise the efficiency of Estonian R
&
D policy and the influence of the socioeconomic environment.

Research limitations/implications
– The lack of comparable data describing R
&
D policy and R
&
D activities and innovation performance in the business sector limits the comprehensiveness of the analysis (i.e. the number of analysed indicators).

Practical implications
– The assessment and comparative analysis of the influence of R
&
D policy components on business sector R
&
D activities and innovation performance in different countries makes it possible to identify directions for increasing the efficiency of R
&
D policy under the specific influence of the socioeconomic environment, especially in new member states of the EU.

Originality/value
– Using the PCA method significantly increased the robustness of the macro-quantitative description of R
&
D policy dimensions. By combining the set of new synthetic R
&
D policy indicators created by the PCA with the multiple regression analysis method, a significant increase in the robustness of model coefficients (i.e. the assessments of influence intensity) was achieved. These robust models create the basis for reliable empirical assessment of the influence of R
&
D policy and a comparative analysis of the results.