bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydroxyurea-inducible SAR1 gene acts through the Giα/JNK/Jun pathway to regulate γ-globin expression
Authors: Zhu Jianqiong , Chin Kyung , Aerbajinai Wulin , Kumkhaek Chutima , Li Hongzhen , Rodgers Griffin P. 
Published: June 2014

Key Points
Hydroxyurea activates nuclear factor–κB to transcriptionally upregulate SAR1. SAR1, in turn, activates γ-globin expression through the Giα/JNK/Jun pathway.
Hematopoietic stem cell transplantation donor sources in the 21st century: choosing the ideal donor when a perfect match does not exist
Authors: Kekre Natasha , Antin Joseph H. 
Published: June 2014

Abstract
Most patients who require allogeneic stem cell transplantation do not have a matched sibling donor, and many patients do not have a matched unrelated donor. In an effort to increase the applicability of transplantation, alternative donors such as mismatched adult unrelated donors, haploidentical related donors, and umbilical cord blood stem cell products are frequently used when a well matched donor is unavailable. We do not yet have the benefit of randomized trials comparing alternative donor stem cell sources to inform the choice of donor; however, the existing data allow some inferences to be made on the basis of existing observational and phase 2 studies. All 3 alternative donor sources can provide effective lymphohematopoietic reconstitution, but time to engraftment, graft failure rate, graft-versus-host disease, transplant-related mortality, and relapse risk vary by donor source. These factors all contribute to survival outcomes and an understanding of them should help guide clinicians when choosing among alternative donor sources when a matched related or matched unrelated donor is not available.
Identification of cereblon-binding proteins and relationship with response and survival after IMiDs in multiple myeloma
Authors: Zhu Yuan Xiao , Braggio Esteban , Shi Chang-Xin , Kortuem K. Martin , Bruins Laura A. , Schmidt Jessica E. , Chang Xiu-Bao , Langlais Paul , Luo Moulun , Jedlowski Patrick , LaPlant Betsy , Laumann Kristina , Fonseca Rafael , Bergsagel P. Leif , Mikhael Joseph , Lacy Martha , Champion Mia D. , Stewart A. Keith 
Published: June 2014

Key PointsWe identified CRBN-binding proteins and confirmed recent work implicating the Ikaros transcription factors as important members. Low IZKF1 levels predict lack of IMiD responsiveness and shorter OS; IZKF1 expression is a potential predictive biomarker for clinic application.
Integrating the interactome and the transcriptome of Drosophila
Authors: Murali Thilakam , Pacifico Svetlana , Finley Russell L 
Published: June 2014

AbstractBackgroundNetworks of interacting genes and gene products mediate most cellular and developmental processes. High throughput screening methods combined with literature curation are identifying many of the protein-protein interactions (PPI) and protein-DNA interactions (PDI) that constitute these networks. Most of the detection methods, however, fail to identify thein vivospatial or temporal context of the interactions. Thus, the interaction data are a composite of the individual networks that may operate in specific tissues or developmental stages. Genome-wide expression data may be useful for filtering interaction data to identify the subnetworks that operate in specific spatial or temporal contexts. Here we take advantage of the extensive interaction and expression data available forDrosophilato analyze how interaction networks may be unique to specific tissues and developmental stages.ResultsWe ranked genes on a scale from ubiquitously expressed to tissue or stage specific and examined their interaction patterns. Interestingly, ubiquitously expressed genes have many more interactions among themselves than do non-ubiquitously expressed genes both in PPI and PDI networks. While the PDI network is enriched for interactions between tissue-specific transcription factors and their tissue-specific targets, a preponderance of the PDI interactions are between ubiquitous and non-ubiquitously expressed genes and proteins. In contrast to PDI, PPI networks are depleted for interactions among tissue- or stage- specific proteins, which instead interact primarily with widely expressed proteins. In light of these findings, we present an approach to filter interaction data based on gene expression levels normalized across tissues or developmental stages. We show that this filter (the percent maximum or pmax filter) can be used to identify subnetworks that function within individual tissues or developmental stages.ConclusionsThese observations suggest that protein networks are frequently organized into hubs of widely expressed proteins to which are attached various tissue- or stage-specific proteins. This is consistent with earlier analyses of human PPI data and suggests a similar organization of interaction networks across species. This organization implies that tissue or stage specific networks can be best identified from interactome data by using filters designed to include both ubiquitously expressed and specifically expressed genes and proteins.
Design of a flexible component gathering algorithm for converting cell-based models to graph representations for use in evolutionary search
Authors: Budnikova Marianna , Habig Jeffrey W , Lobo Daniel , Cornia Nicolas , Levin Michael , Andersen Tim 
Published: June 2014

Abstract

Background
The ability of science to produce experimental data has outpaced the ability to effectively visualize and integrate the data into a conceptual framework that can further higher order understanding. Multidimensional and shape-based observational data of regenerative biology presents a particularly daunting challenge in this regard. Large amounts of data are available in regenerative biology, but little progress has been made in understanding how organisms such as planaria robustly achieve and maintain body form. An example of this kind of data can be found in a new repository (PlanformDB) that encodes descriptions of planaria experiments and morphological outcomes using a graph formalism.

Results
We are developing a model discovery framework that uses a cell-based modeling platform combined with evolutionary search to automatically search for and identify plausible mechanisms for the biological behavior described in PlanformDB. To automate the evolutionary search we developed a way to compare the output of the modeling platform to the morphological descriptions stored in PlanformDB. We used a flexible connected component algorithm to create a graph representation of the virtual worm from the robust, cell-based simulation data. These graphs can then be validated and compared with target data from PlanformDB using the well-known graph-edit distance calculation, which provides a quantitative metric of similarity between graphs. The graph edit distance calculation was integrated into a fitness function that was able to guide automated searches for unbiased models of planarian regeneration. We present a cell-based model of planarian that can regenerate anatomical regions following bisection of the organism, and show that the automated model discovery framework is capable of searching for and finding models of planarian regeneration that match experimental data stored in PlanformDB.

Conclusion
The work presented here, including our algorithm for converting cell-based models into graphs for comparison with data stored in an external data repository, has made feasible the automated development, training, and validation of computational models using morphology-based data. This work is part of an ongoing project to automate the search process, which will greatly expand our ability to identify, consider, and test biological mechanisms in the field of regenerative biology.
Practice of skin protection and skin care among German surgeons and influence on the efficacy of surgical hand disinfection and surgical glove perforation
Authors: Harnoss Julian C , Brune Laura , Ansorg Jörg , Heidecke Claus-Dieter , Assadian Ojan , Kramer Axel 
Published: June 2014

Abstract

Background
Surgical hand rub and healthy skin are basic requirements to prevent surgical site infections. Nevertheless, there is little knowledge about the current practice of skin protection and/or skin care products (SP/SC) using among surgeons as well as a lack of data pertaining to the influence of SP/SC on the antimicrobial efficacy of surgical hand rub.

Methods
A 10 weeks-survey among German surgeons as well as an experimental crossover study involving 26 participants were conducted. The immediate and sustainable efficacy (IE/SE) of surgical hand rub and participants’ hand moisture were measured after an 8-day usage of SP/SC, as well as the influence on micro-perforations on surgical gloves.

Results
The questionnaire was available to 16,000 German surgeons. Thereof, 1,771 surgeons accessed the questionnaire, representing a total participation rate of 11%. As 19% (n = 338) of questionnaires were incomplete, a total of 1,433 completed questionnaires were available for further analysis. More than 75% of the participants stated not to use any SP/SC, yet, almost 50% suffered from skin irritation or discomfort. Only 5% used SP/SC at the beginning of their shift. 10% refused to use SP/SC because of concerns that SP/SC may reduce the antimicrobial efficacy of surgical hand rub.
After usage of SP/SC over 8-days, skin moisture was significantly higher (P < 0.001), whereas no significant influence on the antimicrobial efficacy of surgical hand rub was observed (IE: P = 0.135; SP: P = 0.681). Micro-perforations were detected in 8/52 surgical gloves (15%), with no statistical significant difference between SP/SC users (n = 2/26; 8%) and non-users (n = 6/26; 23%; P = 0.249).

Conclusions
Following the results of this largest questionnaire base survey among German surgeons on skin care, there is a need to educate and inform surgeons on the correct application and the concept of SP/SC strategies. In the present study, the combination of selected SP/SC products and one alcohol-based hand rub formulation did not show a negative interaction with surgical hand rub or surgical glove perforation. However, it is advisable to ascertain the compatibility of SP/SC products with the used hand disinfectant prior to purchase.
Stochastic switching of TiO2-based memristive devices with identical initial memory states
Authors: Li Qingjiang , Khiat Ali , Salaoru Iulia , Xu Hui , Prodromakis Themistoklis 
Published: June 2014

Abstract
In this work, we show that identical TiO2-based memristive devices that possess the same initial resistive states are only phenomenologically similar as their internal structures may vary significantly, which could render quite dissimilar switching dynamics. We experimentally demonstrated that the resistive switching of practical devices with similar initial states could occur at different programming stimuli cycles. We argue that similar memory states can be transcribed via numerous distinct active core states through the dissimilar reduced TiO2-x
filamentary distributions. Our hypothesis was finally verified via simulated results of the memory state evolution, by taking into account dissimilar initial filamentary distribution.
No evidence for LGV transmission among heterosexuals in Amsterdam, the Netherlands
Authors: Heiligenberg Marlies , Verweij Stephan P , Speksnijder Arjen GCL , Morré Servaas A , de Vries Henry JC , Schim van der Loeff Maarten F 
Published: June 2014

Abstract

Background
In recent years a few cases of lymphogranuloma venereum (LGV) in heterosexuals in Europe have been reported. It is not known whether LGV transmission among heterosexuals occurs on a wider scale.

Methods
Heterosexual male and female STI clinic clients (n = 587) in Amsterdam, the Netherlands, with a positive nucleic acid amplification test (NAAT) result for Chlamydia trachomatis (CT) were screened for IgA anti-MOMP in serum. If the value was above the cut-off index (2.0) the patient’s CT positive urogenital, ocular or rectal sample(s) were selected and tested for LGV by an in-house LGV-specific NAAT.

Results
Sera of 126 patients were above 2.0 COI. Some patients had >1 CT positive sample. Samples could not be retrieved from 15 of the 126 persons, and 7 samples that were found positive for CT in the diagnostic amplification process could not be confirmed and hence not typed. We did not find a single case of LGV infection in 123 urogenital, ocular or rectal samples from 104 patients.

Conclusion
We found no indications for significant spread of LGV infection in heterosexuals in Amsterdam. Surveillance in females with cervical or anal CT infection is indicated to monitor LGV occurrence in heterosexuals.
Programmatic Variation in Home Hemodialysis in Canada: Results from a Nationwide Survey of Practice Patterns
Authors: Pauly Robert P , Komenda Paul , Chan Christopher T , Copland Michael , Gangji Azim , Hirsch David , Lindsay Robert , MacKinnon Martin , MacRae Jennifer M , McFarlane Philip , Nesrallah Gihad , Pierratos Andreas , Plaisance Martin , Reintjes Frances , Rioux Jean-Philippe , Shik John , Steele Andrew , Stryker Rod , Wu George , Zimmerman Deborah L 
Published: June 2014

Background: Over 40% of patients with end stage renal disease in the United States were treated with home hemodialysis (HHD) in the early 1970's. However, this number declined rapidly over the ensuing decades so that the overwhelming majority of patients were treated in-centre 3 times per week on a 3–4 hour schedule. Poor outcomes for patients treated in this fashion led to a renewed interest in home hemodialysis, with more intensive dialysis schedules including short daily (SDHD) and nocturnal (NHD). The relative infancy of these treatment schedules means that there is a paucity of data on ‘how to do it’. Objective: We undertook a systematic survey of home hemodialysis programs in Canada to describe current practice patterns. Design: Development and deployment of a qualitative survey instrument. Setting: Community and academic HHD programs in Canada. Participants: Physicians, nurses and technologists. Measurements: Programmatic approaches to patient selection, delivery of dialysis, human resources available, and follow up. Methods: We developed the survey instrument in three phases. A focus group of Canadian nephrologists with expertise in NHD or SDHD discussed the scope the study and wrote questions on 11 domains. Three nephrologists familiar with all aspects of HHD delivery reviewed this for content validity, followed by further feedback from the whole group. Multidisciplinary teams at three sites pretested the survey and further suggestions were incorporated. In July 2010 we distributed the survey electronically to all renal programs known to offer HHD according to the Canadian Organ Replacement Registry. We compiled the survey results using qualitative and quantitative methods, as appropriate. Results: Of the academic and community programs that were invited to participate, 80% and 63%, respectively, completed the survey. We observed wide variation in programmatic approaches to patient recruitment, human resources, equipment, water, vascular access, patient training, dialysis prescription, home requirements, patient follow up, medications, and the approach to non-adherent patients. Limitations: Cross-sectional survey, unable to link variation to outcomes. Competition for patients between HHD and home peritoneal dialysis means that case mix for HHD may also vary between centres. Conclusions: There is wide variation between programs in all domains of HHD delivery in Canada. We plan further study of the extent to which differences in approach are related to outcomes.
Mesenchymal precursor cells maintain the differentiation and proliferation potentials of breast epithelial cells
Authors: Duss Stephan , Brinkhaus Heike , Britschgi Adrian , Cabuy Erik , Frey Daniel M , Schaefer Dirk J , Bentires-Alj Mohamed 
Published: June 2014

Abstract
Introduction
Stromal-epithelial interactions play a fundamental role in tissue homeostasis, controlling cell proliferation and differentiation. Not surprisingly, aberrant stromal-epithelial interactions contribute to malignancies. Studies of the cellular and molecular mechanisms underlying these interactions require ex vivo experimental model systems that recapitulate the complexity of human tissue without compromising the differentiation and proliferation potentials of human primary cells.

Methods
We isolated and characterized human breast epithelial and mesenchymal precursors from reduction mammoplasty tissue and tagged them with lentiviral vectors. We assembled heterotypic co-cultures and compared mesenchymal and epithelial cells to cells in corresponding monocultures by analyzing growth, differentiation potentials, and gene expression profiles.

Results
We show that heterotypic culture of non-immortalized human primary breast epithelial and mesenchymal precursors maintains their proliferation and differentiation potentials and constrains their growth. We further describe the gene expression profiles of stromal and epithelial cells in co-cultures and monocultures and show increased expression of the tumor growth factor beta (TGFβ) family member inhibin beta A (INHBA) in mesenchymal cells grown as co-cultures compared with monocultures. Notably, overexpression of INHBA in mesenchymal cells increases colony formation potential of epithelial cells, suggesting that it contributes to the dynamic reciprocity between breast mesenchymal and epithelial cells.

Conclusions
The described heterotypic co-culture system will prove useful for further characterization of the molecular mechanisms mediating interactions between human normal or neoplastic breast epithelial cells and the stroma, and will provide a framework to test the relevance of the ever-increasing number of oncogenomic alterations identified in human breast cancer.
Mapping-by-sequencing accelerates forward genetics in barley
Authors: Mascher Martin , Jost Matthias , Kuon Joel-Elias , Himmelbach Axel , Aßfalg Axel , Beier Sebastian , Scholz Uwe , Graner Andreas , Stein Nils 
Published: June 2014

AbstractMapping-by-sequencing has emerged as a powerful technique for genetic mapping in several plant and animal species. As this resequencing-based method requires a reference genome, its application to complex plant genomes with incomplete and fragmented sequence resources remains challenging. We perform exome sequencing of phenotypic bulks of a mapping population of barley segregating for a mutant phenotype that increases the rate of leaf initiation. Read depth analysis identifies a candidate gene, which is confirmed by the analysis of independent mutant alleles. Our method illustrates how the genomic resources of barley together with exome resequencing can underpin mapping-by-sequencing.
Effect of Communication Skills Training Program for Oncologists Based on Patient Preferences for Communication When Receiving Bad News: A Randomized Controlled Trial
Authors: Fujimori Maiko , Shirai Yuki , Asai Mariko , Kubota Kaoru , Katsumata Noriyuki , Uchitomi Yosuke 
Published: June 2014

Purpose The aim of this study was to identify the effects of a communication skills training (CST) program for oncologists, developed based on patient preferences regarding oncologists' communication. Participants and Methods Thirty oncologists were randomly assigned to either an intervention group (IG; 2-day CST workshop) or control group (CG). Participants were assessed on their communication performance during simulated consultation and their confidence in communicating with patients at baseline and follow-up. A total of 1,192 patients (response rate, 84.6%) who had consultations with the participating oncologists at baseline and/or follow-up were assessed regarding their distress using the Hospital Anxiety and Depression Scale, satisfaction with the consultation, and trust in their oncologist after the consultation. Results At the follow-up survey, the performance scores of the IG had improved significantly, in terms of their emotional support (P = .011), setting up a supportive environment (P = .002), and ability to deliver information (P = .001), compared with those of the CG. Oncologists in the IG were rated higher at follow-up than those in the CG in terms of their confidence in themselves (P = .001). Patients who met with oncologists after they had undergone the CST were significantly less depressed than those who met with oncologists in the CG (P = .027). However, the CST program did not affect patient satisfaction with oncologists' style of communication. Conclusion A CST program based on patient preferences is effective for both oncologists and patients with cancer. Oncologists should consider CST as an approach to enhancing their communication skills.
Thyroid Hormone Receptor α Mutation Causes a Severe and Thyroxine-Resistant Skeletal Dysplasia in Female Mice
Authors: Bassett J. H. Duncan , Boyde Alan , Zikmund Tomas , Evans Holly , Croucher Peter I. , Zhu Xuguang , Park Jeong Won , Cheng Sheue-yann , Williams Graham R. 
Published: June 2014

Abstract
A new genetic disorder has been identified that results from mutation of THRA, encoding thyroid hormone receptor α1 (TRα1). Affected children have a high serum T3:T4 ratio and variable degrees of intellectual deficit and constipation but exhibit a consistently severe skeletal dysplasia. In an attempt to improve developmental delay and alleviate symptoms of hypothyroidism, patients are receiving varying doses and durations of T4 treatment, but responses have been inconsistent so far. Thra1PV/+ mice express a similar potent dominant-negative mutant TRα1 to affected individuals, and thus represent an excellent disease model. We hypothesized that Thra1PV/+ mice could be used to predict the skeletal outcome of human THRA mutations and determine whether prolonged treatment with a supraphysiological dose of T4 ameliorates the skeletal abnormalities. Adult female Thra1PV/+ mice had short stature, grossly abnormal bone morphology but normal bone strength despite high bone mass. Although T4 treatment suppressed TSH secretion, it had no effect on skeletal maturation, linear growth, or bone mineralization, thus demonstrating profound tissue resistance to thyroid hormone. Despite this, prolonged T4 treatment abnormally increased bone stiffness and strength, suggesting the potential for detrimental consequences in the long term. Our studies establish that TRα1 has an essential role in the developing and adult skeleton and predict that patients with different THRA mutations will display variable responses to T4 treatment, which depend on the severity of the causative mutation.