bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recombinant Staphylococcal Enterotoxin Type A Stimulate Antitumoral Cytokines
Authors: Agheli Reza , Emkanian Bijan , Halabian Raheleh , Fallah Mehrabadi Jalil , Imani Fooladi Abbas Ali 
Published: November 2016

Background: About 20 different types of staphylococcal enterotoxins are produced by Staphylococcus aureus, in which type A is more common in food poisoning syndrome. Also staphylococcal enterotoxin A superantigen is a potent inducer of cytotoxic T lymphocyte activity and cytokine production and could stimulate T cells containing T-cell receptor beta chain domains when binding to major histocompatibility complex class II molecules. Hence, it is an important reagent in cancer immunotherapy. Methods: For the construction of pET-21a/ entA cassette, the staphylococcal enterotoxin type A gene was isolated from S aureus strain HN2, cloned into pET-21a, and introduced into Escherichia coli strain BL-21(DE3). Consequently, Western blot analysis showed pET-21a/ entA cassette expression inserted entA gene successfully. It is the first prompt using a pET-21a as a cloning vector for entA gene and expression of construct in BL-21(DE3). In addition, this study examined the ability of standard staphylococcal enterotoxin A and cloned staphylococcal enterotoxin A to activate T cells in vitro. Lymphocyte cells derived from lymph node BALB/c mice were exposed to standard staphylococcal enterotoxin A and cloned staphylococcal enterotoxin (1.10, 102,103, and 104 ng/µL) in order to evaluate the magnitude of proliferation, activation, and apoptosis of lymphocyte cells based on MTT and apoptosis assays, respectively. Results: Our investigation showed that the function of cloned staphylococcal enterotoxin A was same as standard staphylococcal enterotoxin A, and the optimal concentration for the activation of lymphocyte cells and induction of apoptosis was 100 ng/µL and 1000 ng/µL ( P < .05), respectively. Quantification of cytokines clearly showed that lymphocyte cells exposed to standard staphylococcal enterotoxin A and cloned staphylococcal enterotoxin A significantly secreted higher interferon γ and tumor necrosis factor α compared to control. Conclusion: According to our results, the biological activity of standard staphylococcal enterotoxin A and cloned staphylococcal enterotoxin A is identical; therefore, these procedures may be approved as an efficient method to express and purify this protein in a large scale.
Ruptured abdominal aortic aneurysm after endovascular aortic aneurysm repair thrombosis
Authors: Victory Jesse , Rizvi Syed Ali , Ascher Enrico , Hingorani Anil 
Published: November 2016

Background Complete thrombosis of an aortic endograft after an endovascular aortic aneurysm repair is a rare complication. The majority of thrombotic events occur in the iliac limbs. Case presentation We present the case of a patient who presented with acute limb ischemia as the result of a thrombosed infra-renal aortic endograft. After restoration of blood flow to the lower extremities with an axillary to bi-femoral artery bypass, the patient was lost to follow-up. The patient returned two years later with a ruptured abdominal aortic aneurysm due to a type 1A endoleak. Discussion We propose that all patients after endovascular aortic aneurysm repair, including those with a thrombosed aortic endograft, continue to undergo regular graft surveillance. This case report highlights the importance of continued surveillance of the aortic sac, even after total thrombosis of the endovascular aortic aneurysm repair.
Diet modification challenges faced by marginalized and nonmarginalized adults with type 2 diabetes: A systematic review and qualitative meta-synthesis
Authors: Vanstone Meredith , Rewegan Alex , Brundisini Francesca , Giacomini Mita , Kandasamy Sujane , DeJean Deirdre 
Published: November 2016

Objectives Diet modification is an important part of the prevention and treatment of type 2 diabetes, but sustained dietary change remains elusive for many individuals. This paper describes and interprets the barriers to diet modification from the perspective of people with type 2 diabetes, paying particular attention to the experiences of people who experience social marginalization. Methods A systematic review of primary, empirical qualitative research was performed, capturing 120 relevant studies published between 2002 and 2015. Qualitative meta-synthesis was used to provide an integrative analysis of this knowledge. Results Due to the central role of food in social life, dietary change affects all aspects of a person’s life, and barriers related to self-discipline, emotions, family and social support, social significance of food, and knowledge were identified. These barriers are inter-linked and overlapping. Social marginalization magnifies barriers; people who face social marginalization are trying to make the same changes as other people with diabetes with fewer socio-material resources in the face of greater challenges. Discussion A social-ecological model of behavior supports our findings of challenges at all levels, and highlights the need for interventions and counseling strategies that address the social and environmental factors that shape and sustain dietary change.
Giant Cell Tumor of Talus: T-Construct Method of Bone Grafting
Authors: Kadam Abhijeet B. , Dhamangaonkar Anoop C. 
Published: November 2016

Giant cell tumor (GCT) or osteoclastoma is a benign, locally aggressive tumor with a tendency to recur. Giant cell tumors typically occur in the epiphysis of long bones, including the distal femur and proximal tibia. They are uncommonly found in the small bones of the foot or ankle, and involvement of talus is rare. The authors present a case of GCT of the talar body in a 21-year-old man, which was diagnosed radiologically by the presence of a well-defined osteolytic lesion involving more than half of the talar body with thinning of the cortices. An intralesional curettage and chemical cauterization with phenol was done using a medial approach following an osteotomy of the medial malleolus for adequate exposure. Intraoperative frozen section of curetted tissue was sent and was reported as benign GCT. The residual cavity was packed with autologous corticocancellous bone grafts fashioned in a T-construct like manner. A protective cast was applied for a period of 2 months and patient was subsequently gradually mobilized to full weightbearing status. At 2-year follow-up, there was no clinical or radiologically evident signs of recurrence. There was good consolidation of the bone graft in the talus with no signs of collapse of the weightbearing articular surface. Levels of Evidence: Therapeutic, Level IV: Case Study
Technique Tip: Single-Incision Endoscopic Plantar Fasciotomy
Authors: Thomas Zachary M. , Thomas Kristin J. 
Published: November 2016

Two-incision endoscopic plantar fasciotomy (EPF) is an accepted surgical technique in the treatment of recalcitrant plantar fasciitis. Single-incision plantar fasciotomy is a relatively new technique in the surgeons’ armamentarium; however, it is not without pitfalls, specifically poor visualization. This article aims to help the foot and ankle surgeon make a smooth transition from 2-incision EPF to single-incision EPF while maintaining optimum visualization. Levels of Evidence: Level V: Expert opinion
Risk factors for proximal disease extension and colectomy in left‐sided ulcerative colitis
Authors: Sahami S , Konté K , Buskens CJ , Tanis PJ , Löwenberg M , Ponsioen CJ , van den Brink GR , Bemelman WA , D’Haens GR 
Published: November 2016

ObjectiveThe primary objective of this study was to assess proximal disease extension of ulcerative colitis (UC) over time, with disease behaviour pattern and risk factors for proximal disease extension and colectomy as secondary aims.MethodsAll cumulative incident cases diagnosed with UC at the Academic Medical Center between January 1990 and December 2009 were studied. The cumulative risk of colectomy was calculated by Kaplan‐Meier analysis. The Cox proportional hazards regression was used to identify risk factors associated with proximal disease extension and colectomy.ResultsIn total, 506 UC patients were included with a median age of 33 years (IQR 23–41) at diagnosis. Ninety‐five (18.8%) patients underwent colectomy during follow‐up. Median follow‐up was 10 years (IQR 5–15). Initial disease extent was evaluable in 416 patients, of whom 142 (34.1%) had proctitis, 155 (37.3%) left‐sided colitis and 119 (28.6%) pancolitis. Proximal disease extension was observed in 120 (28.8%) patients during follow‐up (51 proctitis to left‐sided colitis, 39 proctitis to extensive colitis and 30 left‐sided to extensive colitis). Disease behaviour was evaluable in 378 patients, of whom 244 (64.6%) had less than one relapse per year. Younger age at diagnosis (HR 0.98, 95% CI 0.96–0.99) and continuous active disease (HR 2.18, 95% CI 1.27–3.73) were independent risk factors for proximal disease extension. The cumulative risk of colectomy did not change over time between patients diagnosed before and after the year 2000 (p  = 0.341). Continuous active disease (HR 7.05, 95% CI 4.23–11.77), systemic steroids (HR 3.25, 95% CI 1.37–7.71) and cyclosporine treatment (HR 2.80, 95% CI 1.66–4.72) were independent risk factors for colectomy, whereas proctitis at diagnosis (HR 0.43, 95% CI 0.22–0.86) carried a lower risk.ConclusionIn one‐third of UC patients, left‐sided disease at diagnosis will extend proximally during 10 years of follow‐up. Proximal disease extension was not a risk factor for colectomy, but the risk of colectomy is rather determined by continuous disease activity, and use of systemic steroids and cyclosporine.
Flow cytometry of duodenal intraepithelial lymphocytes improves diagnosis of celiac disease in difficult cases
Authors: Valle Julio , Morgado José Mario T , Ruiz‐Martín Juan , Guardiola Antonio , Lopes‐Nogueras Miriam , García‐Vela Almudena , Martín‐Sacristán Beatriz , Sánchez‐Muñoz Laura 
Published: November 2016

BackgroundDiagnosis of celiac disease is difficult when the combined results of serology and histology are inconclusive. Studies using flow cytometry of intraepithelial lymphocytes (IELs) have found that celiac patients have increased numbers of γδ IELs, along with a decrease in CD3‐CD103 + IELs.ObjectiveThe objective of this article is to assess the role of flow cytometric analysis of IELs in the diagnosis of celiac disease in difficult cases.MethodsA total of 312 patients with suspicion of celiac disease were included in the study. Duodenal biopsy samples were used for histological assessment and for flow cytometric analysis of IELs.ResultsIn 46 out of 312 cases (14.7%) the combination of serology and histology did not allow the confirmation or exclusion of celiac disease. HLA typing had been performed in 42 of these difficult cases. Taking into account HLA typing and the response to a gluten‐free diet, celiac disease was excluded in 30 of these cases and confirmed in the remaining 12. Flow cytometric analysis of IELs allowed a correct diagnosis in 39 out of 42 difficult cases (92.8%) and had a sensitivity of 91.7% (95% CI: 61.5% to 99.8%) and a specificity of 93.3% (95% CI: 77.9% to 99.2%) for the diagnosis of celiac disease in this setting.ConclusionFlow cytometric analysis of IELs is useful for the diagnosis of celiac disease in difficult cases.
‘Pushed’ self-tracking using digital technologies for chronic health condition management: a critical interpretive synthesis
Authors: Morgan Heather 
Published: November 2016

Introduction Health policies internationally advocate health services provider support for health services users’ ‘self-management’ of chronic health conditions. Digital technologies are beginning to have a role in delivering such support. ‘Pushed’ self-tracking of health-related information, including imposed measurement of biomedical and behavioural data, is one approach; however, there is little systematic or discursive research. The aim of this research was to explore factors relevant to the implementation of ‘pushed’ self-tracking technologies into support for self-management of chronic health conditions interventions. Methods This paper reports a critical interpretive synthesis of studies involving ‘pushed’ self-tracking using digital technologies to support the self-management of chronic health conditions. The review systematically identified relevant literature, characterised the technologies and discursively explored their implementation and impacts, and human technology interactions. Findings The literature ( n = 83), including ‘simple’ ( n = 51) and ‘complex’ ( n = 32) interventions, perhaps unsurprisingly, concentrates on technical and clinical rather than sociological and behavioural perspectives, which limits understanding. Some attention is paid to experiences and views of providers and users about digital technologies implementation and impacts on the delivery of care, for example: consequences of having increased information; compatibility with current systems; implications for personnel; and human–technology negotiations. Conclusions This is a rapidly developing field and early technical and clinical insights are useful. There are opportunities for researchers to explore the sociological and behavioural aspects, and ethical challenges, of implementing ‘pushed’ self-tracking support programmes too. Detailed multidisciplinary research is needed to understand and guide technical and medical developments that integrate digital technologies into the delivery of care.
Electromagnetic inductance plethysmography is well suited to measure tidal breathing in infants
Authors: Bentsen Mariann H.L. , Eriksen Morten , Olsen Merete S. , Markestad Trond , Halvorsen Thomas 
Published: November 2016

Reliable, accurate and noninvasive methods for measuring lung function in infants are desirable. Electromagnetic inductance plethysmography has been used to perform infant spirometry and VoluSense Pediatrics (VSP) (VoluSense, Bergen, Norway) represents an updated version of this technique. We aimed to examine its accuracy compared to a validated system measuring airflowviaa facemask using an ultrasonic flowmeter.We tested 30 infants with postmenstrual ages between 36 to 43 weeks and weights from 2.3 to 4.8 kg, applying both methods simultaneously and applying VSP alone. Agreement between the methods was calculated using Bland–Altman analyses and we also estimated the effect of applying the mask.Mean differences for all breathing parameters were within ±5.5% and limits of agreement between the two methods were acceptable, except perhaps for peak tidal expiratory flow (PTEF). Application of the facemask significantly increased tidal volume, minute ventilation, PTEF, the ratio of inspiratory to expiratory time and the ratio of expiratory flow at 50% of expired volume to PTEF.VSP accurately measured tidal breathing parameters and seems well suited for tidal breathing measurements in infants under treatment with equipment that precludes the use of a facemask.
SPECtre: a spectral coherence-­based classifier of actively translated transcripts from ribosome profiling sequence data
Authors: Chun Sang Y. , Rodriguez Caitlin M. , Todd Peter K. , Mills Ryan E. 
Published: November 2016

Abstract
Background
Active protein translation can be assessed and measured using ribosome profiling sequencing strategies. Prevailing analytical approaches applied to this technology make use of sequence fragment length profiling or reading frame occupancy enrichment to differentiate between active translation and background noise, however they do not consider additional characteristics inherent to the technology which limits their overall accuracy.

Results
Here, we present an analytical tool that models the overall tri­nucleotide periodicity of ribosomal occupancy using a classifier based on spectral coherence. Our software, SPECtre, examines the relationship of normalized ribosome profiling read coverage over a rolling series of windows along a transcript relative to an idealized reference signal without the matched requirement of mRNA-Seq.

Conclusions
A comparison of SPECtre against previously published methods on existing data shows a marked improvement in accuracy for detecting active translation and exhibits overall high accuracy at a low false discovery rate. In addition, SPECtre performs comparably to a recently published method similarly based on spectral coherence, however with reduced runtime and memory requirements. SPECtre is available as an open source software package at https://github.com/mills-lab/spectre.
A new method of finding groups of coexpressed genes and conditions of coexpression
Authors: Anand Rajat , Ravichandran Srikanth , Chatterjee Samrat 
Published: November 2016

Abstract
Background
To study a biological phenomenon such as finding mechanism of disease, common methodology is to generate the microarray data in different relevant conditions and find groups of genes co-expressed across conditions from such data. These groups might enable us to find biological processes involved in a disease condition. However, more detailed understanding can be made when information of a biological process associated with a particular condition is obtained from the data. Many algorithms are available which finds groups of co-expressed genes and associated conditions of co-expression that can help finding processes associated with particular condition. However, these algorithms depend on different input parameters for generating groups. For real datasets, it is difficult to use these algorithms due to unknown values of these parameters.

Results
We present here an algorithm, clustered groups, which finds groups of co-expressed genes and conditions of co-expression with minimal input from user. We used random datasets to derive a cutoff on the basis of which we filtered the resultant groups and showed that this can improve the relevance of obtained groups. We showed that the proposed algorithm performs better than other known algorithms on both real and synthetic datasets. We have also shown its application on a temporal microarray dataset by extracting biclusters and biological information hidden in those biclusters.

Conclusions
Clustered groups is an algorithm which finds groups of co-expressed genes and conditions of co-expression using only a single parameter. We have shown that it works better than other existing algorithms. It can be used to find these groups in different data types such as microarray, proteomics, metabolomics etc.
FluxFix: automatic isotopologue normalization for metabolic tracer analysis
Authors: Trefely Sophie , Ashwell Peter , Snyder Nathaniel W. 
Published: November 2016

Abstract
Background
Isotopic tracer analysis by mass spectrometry is a core technique for the study of metabolism. Isotopically labeled atoms from substrates, such as [13C]-labeled glucose, can be traced by their incorporation over time into specific metabolic products. Mass spectrometry is often used for the detection and differentiation of the isotopologues of each metabolite of interest. For meaningful interpretation, mass spectrometry data from metabolic tracer experiments must be corrected to account for the naturally occurring isotopologue distribution. The calculations required for this correction are time consuming and error prone and existing programs are often platform specific, non-intuitive, commercially licensed and/or limited in accuracy by using theoretical isotopologue distributions, which are prone to artifacts from noise or unresolved interfering signals.

Results
Here we present FluxFix (http://fluxfix.science), an application freely available on the internet that quickly and reliably transforms signal intensity values into percent mole enrichment for each isotopologue measured. ‘Unlabeled’ data, representing the measured natural isotopologue distribution for a chosen analyte, is entered by the user. This data is used to generate a correction matrix according to a well-established algorithm. The correction matrix is applied to labeled data, also entered by the user, thus generating the corrected output data. FluxFix is compatible with direct copy and paste from spreadsheet applications including Excel (Microsoft) and Google sheets and automatically adjusts to account for input data dimensions. The program is simple, easy to use, agnostic to the mass spectrometry platform, generalizable to known or unknown metabolites, and can take input data from either a theoretical natural isotopologue distribution or an experimentally measured one.

Conclusions
Our freely available web-based calculator, FluxFix (http://fluxfix.science), quickly and reliably corrects metabolic tracer data for natural isotopologue abundance enabling faster, more robust and easily accessible data analysis.
Modelling of thermomechanical behaviour of fibrous polymeric composite materials subject to relaxation transition in the matrix
Authors: Matveenko Valeriy Pavlovich , Trufanov Nikolay Alexandrovich , Smetannikov Oleg Yurievich , Shardakov Igor Nikolaevich , Vasserman Igor Nikolaevich 
Published: November 2016

Abstract
Background
Fiber–reinforced polymer composite materials are widely used in different branches of industry due to their distinctive features such as high specific strength and stiffness and due to as considerable opportunity to formulate materials with controllable variation of properties in response to the action of external factors (smart-materials). A distinguishing feature of products made of composite materials is that the processes of product and material fabrication are inseparable. Therefore the estimation of composite properties based on the composite architecture and properties of the reinforcing fibers and matrix is a very actual task.

Methods
The model of polymer behavior at glass transition recently developed by the authors was generalized to the case of fiber-reinforced polymer matrix composites using two approaches: one is base on the concept of free specific energy, the other – on the growth of matrix stiffness. For homogeneous materials these two approaches are of equal worth, whereas for composite materials they give different results under deformation in the transverse direction. The stiffness growth approach is more accurate, but is very expensive computationally and, is highly sensitive to the experimental data errors.

Results
Using the finite element method and averaging technique the thermoelastic constants of composites containing different types of fibers in the glassy and high-elastic states were calculated based on the fiber and matrix properties. Softening of the matrix has an insignificant effect on the longitudinal modulus of a composite but leads to a considerable decrease of the transverse and shear moduli. The coefficient of thermal expansion in the transverse direction is much higher than the coefficient of thermal expansion in the longitudinal direction, especially when the composite is in the high-elastic state.

Conclusion
The model of polymer behavior at glass transition recently developed by the authors can be generalized to the case of fiber-reinforced polymer matrix composites. The thermoelastic constants of composites containing different types of fibers can be calculated from the fiber and matrix properties using the finite element method and averaging technique.