bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk factors for complications in patients with ulcerative colitis
Authors: Manser Christine N , Borovicka Jan , Seibold Frank , Vavricka Stephan R , Lakatos Peter L , Fried Michael , Rogler Gerhard ,   investigators of the Swiss Inflammatory Bowel Disease Cohort Study
Published: January 2016

BackgroundPatients with ulcerative colitis may develop extraintestinal manifestations like erythema nodosum or primary sclerosing cholangitis or extraintestinal complications like anaemia, malabsorption or they may have to undergo surgery.ObjectiveThe aim of this study was to investigate potential risk factors for complications like anaemia, malabsorption or surgery in ulcerative colitis.MethodsData on 179 patients with ulcerative colitis were retrieved from our cross‐sectional and prospective Swiss Inflammatory Bowel Disease Cohort Study data base for a median observational time of 4.2 years. Data were compared between patients with (n  = 140) or without (n  = 39) complications. Gender, age at diagnosis, smoking status, disease extent, delay of diagnosis or therapy, mesalamine (5‐ASA) systemic and topical therapy, as well as other medication were analysed as potential impact factors.ResultsIn the multivariate regression analysis a delay of 5‐ASA treatment by at least two months (odds ratio (OR) 6.21 (95% confidence interval (CI) 2.13–18.14), p  = 0.001) as well as a delay with other medication with thiopurines (OR 6.48 (95% CI 2.01–20.91), p  = 0.002) were associated with a higher risk for complications. This significant impact of a delay of 5‐ASA therapy was demonstrated for extraintestinal manifestations (EIMs) as well as extraintestinal complications (EICs). Extensive disease as well as therapy with methotrexate showed a significantly increased risk for surgery (extensive disease: OR 2.62 (1.02–6.73), p  = 0.05, methotrexate: OR 5.36 (1.64–17.58), p  = 0.006).ConclusionsA delay of 5‐ASA therapy of more than two months in the early stage of ulcerative colitis (UC) constitutes a risk for complications during disease course. Extensive disease is associated with a higher risk for surgery.
Linkage between the mechanisms of thrombocytopenia and thrombopoiesis
Authors: Eto Koji , Kunishima Shinji 
Published: January 2016

Abstract
Thrombocytopenia is defined as a status in which platelet numbers are reduced. Imbalance between the homeostatic regulation of platelet generation and destruction is 1 potential cause of thrombocytopenia. In adults, platelet generation is a 2-stage process entailing the differentiation of hematopoietic stem cells into mature megakaryocytes (MKs; known as megakaryopoiesis) and release of platelets from MKs (known as thrombopoiesis or platelet biogenesis). Until recently, information about the genetic defects responsible for congenital thrombocytopenia was only available for a few forms of the disease. However, investigations over the past 15 years have identified mutations in genes encoding >20 different proteins that are responsible for these disorders, which has advanced our understanding of megakaryopoiesis and thrombopoiesis. The underlying pathogenic mechanisms can be categorized as (1) defects in MK lineage commitment and differentiation, (2) defects in MK maturation, and (3) defect in platelet release. Using these developmental stage categories, we here update recently described mechanisms underlying megakaryopoiesis and thrombopoiesis and discuss the association between platelet generation systems and thrombocytopenia.
Genomic landscape of megakaryopoiesis and platelet function defects
Authors: Bianchi Elisa , Norfo Ruggiero , Pennucci Valentina , Zini Roberta , Manfredini Rossella 
Published: January 2016

Abstract
Megakaryopoiesis is a complex, stepwise process that takes place largely in the bone marrow. At the apex of the hierarchy, hematopoietic stem cells undergo a number of lineage commitment decisions that ultimately lead to the production of polyploid megakaryocytes. On average, megakaryocytes release 1011 platelets per day into the blood that repair vascular injuries and prevent excessive bleeding. This differentiation process is tightly controlled by exogenous and endogenous factors, which have been the topics of intense research in the hematopoietic field. Indeed, a skewing of megakaryocyte commitment and differentiation may entail the onset of myeloproliferative neoplasms and other preleukemic disorders together with acute megakaryoblastic leukemia, whereas quantitative or qualitative defects in platelet production can lead to inherited platelet disorders. The recent advent of next-generation sequencing has prompted mapping of the genomic landscape of these conditions to provide an accurate view of the underlying lesions. The aims of this review are to introduce the physiological pathways of megakaryopoiesis and to present landmark studies on acquired and inherited disorders that target them. These studies have not only introduced a new era in the fields of molecular medicine and targeted therapies but may also provide us with a better understanding of the mechanisms underlying normal megakaryopoiesis and thrombopoiesis that can inform efforts to create alternative sources of megakaryocytes and platelets.
An integrative analysis of gene expression and molecular interaction data to identify dys-regulated sub-networks in inflammatory bowel disease
Authors: Muraro Daniele , Simmons Alison 
Published: January 2016

Abstract
Background
Inflammatory bowel disease (IBD) consists of two main disease-subtypes, Crohn’s disease (CD) and ulcerative colitis (UC); these subtypes share overlapping genetic and clinical features. Genome-wide microarray data enable unbiased documentation of alterations in gene expression that may be disease-specific. As genetic diseases are believed to be caused by genetic alterations affecting the function of signalling pathways, module-centric optimisation algorithms, whose aim is to identify sub-networks that are dys-regulated in disease, are emerging as promising approaches.

Results
In order to account for the topological structure of molecular interaction networks, we developed an optimisation algorithm that integrates databases of known molecular interactions with gene expression data; such integration enables identification of differentially regulated network modules. We verified the performance of our algorithm by testing it on simulated networks; we then applied the same method to study experimental data derived from microarray analysis of CD and UC biopsies and human interactome databases. This analysis allowed the extraction of dys-regulated subnetworks under different experimental conditions (inflamed and uninflamed tissues in CD and UC). Optimisation was performed to highlight differentially expressed network modules that may be common or specific to the disease subtype.

Conclusions
We show that the selected subnetworks include genes and pathways of known relevance for IBD; in particular, the solutions found highlight cross-talk among enriched pathways, mainly the JAK/STAT signalling pathway and the EGF receptor signalling pathway. In addition, integration of gene expression with molecular interaction data highlights nodes that, although not being differentially expressed, interact with differentially expressed nodes and are part of pathways that are relevant to IBD. The method proposed here may help identifying dys-regulated sub-networks that are common in different diseases and sub-networks whose dys-regulation is specific to a particular disease.
Differential requirement of bone morphogenetic protein receptors Ia (ALK3) and Ib (ALK6) in early embryonic patterning and neural crest development
Authors: Schille Carolin , Heller Jens , Schambony Alexandra 
Published: January 2016

Abstract
Background
Bone morphogenetic proteins regulate multiple processes in embryonic development, including early dorso-ventral patterning and neural crest development. BMPs activate heteromeric receptor complexes consisting of type I and type II receptor-serine/threonine kinases. BMP receptors Ia and Ib, also known as ALK3 and ALK6 respectively, are the most common type I receptors that likely mediate most BMP signaling events. Since early expression patterns and functions in Xenopus laevis development have not been described, we have addressed these questions in the present study.

Results
Here we have analyzed the temporal and spatial expression patterns of ALK3 and ALK6; we have also carried out loss-of-function studies to define the function of these receptors in early Xenopus development. We detected both redundant and non-redundant roles of ALK3 and ALK6 in dorso-ventral patterning. From late gastrula stages onwards, their expression patterns diverged, which correlated with a specific, non-redundant requirement of ALK6 in post-gastrula neural crest cells. ALK6 was essential for induction of neural crest cell fate and further development of the neural crest and its derivatives.

Conclusions
ALK3 and ALK6 both contribute to the gene regulatory network that regulates dorso-ventral patterning; they play partially overlapping and partially non-redundant roles in this process. ALK3 and ALK6 are independently required for the spatially restricted activation of BMP signaling and msx2 upregulation at the neural plate border, whereas in post-gastrula development ALK6 exerts a highly specific, conserved function in neural crest development.
In-vitro fertilization and spontaneous pregnancies: matching outcomes in Douala, Cameroon
Authors: Egbe Thomas Obinchemti , Sandjon Guy , Ourtchingh Clovis , Simo André , Priso Eugene Belley , Benifla Jean-Louis 
Published: January 2016

Abstract
Background
Couples are considered infertile if they do not conceive over a 12-month period of unprotected intercourse. Studies have shown that female causes accounted for between 25 to 37 percent of infertility worldwide (with larger proportions in sub-Saharan Africa and Southeast Asia) and male causes accounted for between 8 to 22 percent. Both male and female causes accounted for between 21 to 38 percent. Although the majority of ART children are normal, there are concerns about the increased risk for adverse pregnancy outcomes. More than 30 % of ART pregnancies are twins or higher-order multiple gestations (triplets or greater) and more than one half of all ART neonates are the products of multifetal gestations, with an attendant increase in prematurity complications. The aim of this study was to evaiuate the outcome of pregnancies conceived by In-vitro fertilisation compared to those conceived naturally in two hospitals in Douala, Cameroon.

Methods
This was a prospective study carried out from October 1, 2011 to September 30, 2012. Participants were recruited from two hospitals: the Douala General Hospital (DGH) and the Clinique de l’ Aéroport (CDA), also in Douala. A total of 102 women were recruited for study: 51 who conceived by IVF (cases) and 51 who conceived naturally (controls). Of the 102 women, 52.9 % were between 31 – 39 years of age, while 21.6 % were above 40.

Results
Participants who conceived through IVF-ET were 4.1 times more likely to undergo cesarean delivery than those who conceived naturally [OR 4.10, 95 % CI 1.78–9.42]. Similarly, a higher percentage of patients in the IVF group than those in the control group have never given birth (33.3 % vs 2.0 %) (P < 0.0001). The percentage of multiple pregnancies was 7.5 times higher in the IVF group than in the control group (14.7 % vs.1.96 %) (P = 0.000).
The leading indication for cesarean delivery was advanced maternal age (27.3 %) followed by IVF or precious pregnancy (18.2 %).

Conclusions
Cesarean delivery was more frequent amongst the IVF group than in the control group. The leading indications for cesarean delivery were advanced maternal age and IVF or precious pregnancy.
The long-term neonatal outcomes of IVF babies beyond 5-min Apgar scores should be studied in Cameroon and follow-up beyond 1 year encouraged.
Robust Scheduling Practices in the U.S. Airline Industry: Costs, Returns, and Inefficiencies
Authors: Atkinson Scott E. , Ramdas Kamalini , Williams Jonathan W. 
Published: January 2016

Airlines use robust scheduling to mitigate the impact of unforeseeable disruptions on profits. We examine how effectively three common practices—flexibility to swap aircraft, flexibility to reassign gates, and scheduled aircraft downtime—accomplish this goal. We first estimate a multiple-input, multiple-outcome production frontier, which defines the attainable set of outcomes from given inputs. We then recover unobserved input costs and calculate how expenditure on inputs affects outcomes and revenues. We find that the per-dollar return from expenditure on gates, or more effective management of existing gate capacity, is three times larger than the per-dollar returns from other inputs. Next, we use the estimated trade-offs faced by carriers along the frontier to measure the value to carriers of reducing delays. Finally, we calculate the improvement in carriers’ outcomes and profits if their operational inefficiencies are eliminated. On average, we estimate that operational inefficiencies cost carriers about $1.7 billion in revenue annually. This paper was accepted by Serguei Netessine, operations management.
Patient-performed extraction of faecal calprotectin
Authors: Kristensen Vendel , Lauritzen Trine , Jelsness-Jørgensen Lars-Petter , Frigstad Svein Oskar , Corwin Christian , Moum Bjørn 
Published: January 2016

AbstractFaecal (f-) calprotectin is a widely used marker for intestinal inflammation. However, extraction procedure is time consuming and cumbersome. The main aim of this study was to evaluate patient-performed extraction of f-calprotectin compared to extraction performed in the laboratory.A total of 81 adult patients with an established diagnosis of inflammatory bowel disease provided two samples from the same bowel movement, one conventional faeces sample and one sample with a patient administered extraction device. A laboratory technician extracted the conventional faeces sample with the same extraction device.F-calprotectin results from the laboratory-performed extraction and the patient-performed extraction correlated significantly, with a Spearman rank correlation coefficient of 0.92. Method comparison showed a slope of 1.20 (95% confidence interval 1.08–1.36) with intercept of –0.30 (95% confidence interval –9.00 to 4.62). This demonstrates a small proportional difference between the results from the home extracted samples and the results from the laboratory extracted samples, where the home extracted samples are slightly higher. However, six of the 81 patients had made obvious mistakes in the extraction process and their samples were excluded from the study.Patient administered extraction of f-calprotectin can be a realistic alternative for selected patients. However, instructions must be very precise to avoid mistakes.
Patient identification and tube labelling – a call for harmonisation
Authors: van Dongen-Lases Edmée C. , Cornes Michael P. , Grankvist Kjell , Ibarz Mercedes , Kristensen Gunn B.B. , Lippi Giuseppe , Nybo Mads , Simundic Ana-Maria , on behalf of the Working Group for Preanalytical Phase (WG-P  
Published: January 2016

Abstract
Venous blood sampling (phlebotomy) is the most common invasive procedure performed in patient care. Guidelines on the correct practice of phlebotomy are available, including the H3-A6 guideline issued by the Clinical Laboratory Standards Institute (CLSI). As the quality of practices and procedures related to venous blood sample collection in European countries was unknown, the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) Working Group for the Preanalytical Phase conducted an observational study in 12 European countries. The study demonstrated that the level of compliance of phlebotomy procedures with the CLSI H3-A6 guideline was unacceptably low, and that patient identification and tube labelling are amongst the most critical steps in need of immediate attention and improvement. The process of patient identification and tube labelling is an essential safety barrier to prevent patient identity mix-up. Therefore, the EFLM Working Group aims to encourage and support worldwide harmonisation of patient identification and tube labelling procedures in order to reduce the risk of preanalytical errors and improve patient safety. With this Position paper we wish to raise awareness and provide recommendations for proper patient and sample identification procedures.
Research of foraging and resting behaviour of European ground squirrel (<italic>Spermophilus citellus</italic>) in conditions of zoological garden as a tool for its restitution back to the wild
Authors: Fraňová Sandra , Baláž Ivan 
Published: January 2016

Abstract
We decided to focus our research on two basic forms of behaviour occurring in colonies of ground squirrels in semi-natural conditions of zoological gardens-foraging and resting behaviour.
Our main goal was to perform an analysis of behaviour of ground squirrels living in captivity and to compare these two categories of behaviour on a set timeline. Our research has been performed throughout the span of years 2011and 2012, during which we were able to observe two separate ground squirrel colonies (A, B). In the analytical part, we described the two main forms of ground squirrels’ behaviour in Zoo Bojnice and we subjected the compiled information to a thorough statistical analysis with the aid of main comparison tools. Based on long-term observation and the analysis of the results, we were able to gather detailed information about the two behaviour categories and their duration within a time frame.
The results from the year 2011 confirmed that ground squirrel’s behaviour, bred in captivity, the display of foraging behaviour is the most frequent during the day, as was also observed in wild ground squirrels recorded by Ambros (Ambros, 1999). Within the year 2011 (without human activity) foraging behaviour reaches two peaks with raised frequencies of display, in the daily time periods, the first from 9 to 11 am and the second from 2.30 to 5 pm. We noted a change in behaviour in 2012, when there was a reconstruction nearby the enclosures. These reconstructive activities influenced the behaviour (significant decrease of activity) of the ground squirrels in the presence of the assigned workers approximately until 3 pm, from which time-also in connection with the lessening of the worker’s presence-the foraging behaviour of ground squirrels began to rise rapidly, which held the peak on until 5 pm. Resting behaviour had only one peak with rising trend during the day in dependence on rising temperature of bedding in the enclosure, on which ground squirrels used to sunbathe. These findings give us valuable information about ground squirrels’ behaviour in captivity as well as behaviour influenced by human presence, what can be used in behavioural research of ground squirrels in the wild.
Preservation of authenticity and determination of identity of landscape ecology as one prerequisite of its future development (selected theoretical and meta-scientific aspects)
Authors: Žigrai Florin 
Published: January 2016

Abstract
Authenticity and identity of landscape ecology is the core and synthesis of inherent conditions determining its development. Bringing into line the development of the theory, methodology and application it is possible to strengthen the social and scientific relevance of landscape ecology as the reflection of its theoretical-applied and educational maturity or development. Preservation of authenticity and determination of identity of landscape ecology depend first of all on the relationship between landscape-ecological research object (what is researched), landscape-ecological research approach (how it is researched) and landscape-ecological research subject (who researches). These three parts of landscape-ecological research are subject to a permanent development and change. The delineated meta-scientific, e.g. universal remarks seem to be applicable in an effort to ensure the preservation of the authenticity and identity as the condition of further development for the science solving the ecological-environmental and socio-economical problems in the landscape.
Ecologically Active Surfaces, Methodological Approach to the Study of Ecological Functions
Authors: Terek Jozef , Dobrovič Ján 
Published: January 2016

Abstract
In studies of individual organisation levels of organisms, the requirement of hollistic expression of structure and function is traditional despite the fact that structural direction prevails in studies. Less attention is paid to the place where function activity occurs in connection with the structure. This place is the surface - the medium where physical, chemical, biological and synergic processes interact. These surfaces are called ecologically active surfaces (EAS). From this standpoint, the surface is a place for energy exchange, which appears as mean studies of function and structural properties of the biological object.

The quantification of these areas taking into account the functional activities - (developed surface, the functional characteristics) to the desktop, or to the volume is the methodological starting point in the assessment of the country, or of its componens after the assessment of the energy potential of the environment. This ratio can be considered as the degree of heterogeneity of the conditions after taking into account the gradient of the environment.
We have achieved partial results related to EAS during the solution of tasks connected with the environmental evaluation of biotic components of a landscape, mainly during the investigation of aquatic biotopes, which are demonstrated on some examples.
Species Structure of Plants in the Báb Forest after Logging
Authors: Pilková Ivana 
Published: January 2016

Abstract
In the submitted paper, we have summarised the results of a research that was realised in the locality of the Báb forest (village Veľky Báb, Nitra loess upland). In the area of Báb forest, we were able to document 134 higher plants on 32 permanent research plots (PRP) during 2013. One hundred and twenty-three taxa were documented in the PRP areas situated on clearcuts, whil only 75 were found in the PRP areas located in forest covers. On PRP of clearcuts, there was the highest cover of herb layer; on the other hand, in the forest cover, there was a higher cover of shrub and tree layer. The highest differences in life-forms between two groups of PRP (clearcuts/forest) were detected by hemicryptophytes and terophytes. On all the 32 areas, the biggest number of species belonged to the indigenous species and apophytes. The biggest differences between forests and clearcuts are shown in a representation of C- strategies. The species composition of the Báb forest has changed mainly due to creation of clearcut areas in November 2006. The logging created suitable conditions for the penetration of heliophilious non-indigenous species from the surrounding (mainly anthropogenic) habitats. That is why there are largely synanthropic and non-indigenous taxa represented on permanent clearcut areas, which are spreading further to the forest cover as well as distant areas of the Báb forest.