bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-efficiency nuclear transformation of the oleaginous marine Nannochloropsis species using PCR product
Authors: Li Fengjuan , Gao Dawen , Hu Hanhua 
Published: May 2014

Abstract
Nannochloropsis are model species for investigating biofuel production by algae. To develop them into an integrated photons-to-fuel production platform, high efficiency transformation methods are necessary. Here, we obtained the β-tubulin promoter regions of all recognized species of genus Nannochloropsis, and successfully transformed all five marine species by electroporation. In addition, the PCR amplified double stranded DNA fragments (PCR fragments) based transformation system was established in these Nannochloropsis species, which showed much higher transformation efficiency (10.7–61.2 × 10−6, 1.5–13-fold) than that of linearized plasmid based transformation. The cotransformation of N. salina using a circular plasmid containing a non-selectable GUS gene and a PCR fragment containing only a selection marker cassette was also achieved and found to be very efficient (over 50%). This simple and highly efficient transformation protocol reported in our study provided a useful tool for gene functional analysis and genetic engineering of the oleaginous Nannochloropsis species.
Why fat is so preferable: from oral fat detection to inducing reward in the brain
Authors: Fushiki Tohru 
Published: May 2014

Abstract
Potential mechanisms underlying the high palatability of fat can be assessed by reviewing animal studies on fat detection and brain patterns during reward behavior. Fatty acids are likely recognized by receptors on taste buds, with the signals transmitted to the brain through taste nerves. Ingested oil is broken down and absorbed in the gastrointestinal tract, which also sends signals to the brain through unknown mechanisms. Information from both sensory receptors and peripheral tissue is integrated by the brain, resulting in a strong appetite for fatty foods via a reward system. Understanding mechanisms of fat recognition will prove valuable in the development of strategies to manage the high palatability of foods.
Reference-free prediction of rearrangement breakpoint reads
Authors: Wijaya Edward , Shimizu Kana , Asai Kiyoshi , Hamada Michiaki 
Published: May 2014

Abstract
Motivation : Chromosome rearrangement events are triggered by atypical breaking and rejoining of DNA molecules, which are observed in many cancer-related diseases. The detection of rearrangement is typically done by using short reads generated by next-generation sequencing (NGS) and combining the reads with knowledge of a reference genome. Because structural variations and genomes differ from one person to another, intermediate comparison via a reference genome may lead to loss of information.
Results : In this article, we propose a reference-free method for detecting clusters of breakpoints from the chromosomal rearrangements. This is done by directly comparing a set of NGS normal reads with another set that may be rearranged. Our method SlideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing depth of 100×, it finds ∼88% of the breakpoints correctly with no false-positive reads. Moreover, evaluation on a real prostate cancer dataset shows that the proposed method predicts more fusion transcripts correctly than previous approaches, and yet produces fewer false-positive reads. To our knowledge, this is the first method to detect breakpoint reads without using a reference genome.
Availability and implementation : The source code of SlideSort-BPR can be freely downloaded from https://code.google.com/p/slidesort-bpr/ .
Contact : ewijaya@ifrec.osaka-u.ac.jp or mhamada@waseda.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Outcomes After Curative Thoracic Radiotherapy in Patients With Coronary Artery Disease and Existing Cardiac Stents
Authors: Sio Terence T. , Liang Jackson J. , Chang Kenneth , Novotny Paul J. , Prasad Abhiram , Miller Robert C. 
Published: May 2014

Objectives:
To evaluate outcomes among cancer patients with preexisting coronary artery disease and cardiac stenting who subsequently underwent thoracic radiotherapy (RT).

Methods:
From 1998 to 2012, 147 patients received percutaneous coronary intervention (PCI) and then curative external beam RT (>30 Gy, except for Hodgkin lymphoma patients) involving the heart and the lungs. Heart-specific and lung-specific dosimetric parameters were correlated to overall survival (OS) and cardiac-specific survival by Cox variate methods.

Results:
The mean interval between PCI and cancer diagnosis was 1.8 years (range, 0.1 to 14.2 y). Hypertension was present in 105 patients (71%), and hyperlipidemia in 82 (56%). At the time of analysis, 69 patients (47%) were alive, 3 (2%) died of cardiac causes, and 53 (36%) died of cancer. In multivariate analyses, OS since PCI was related to cancer type (P=0.004). Decreased OS since cancer diagnosis was related to older age (P<0.001) and increased percentage of targeted volume or organ receiving 20 Gy or more for lung (P<0.001), even after controlling for sex, cancer type, and stage. However, for non–cancer-specific survival and major adverse cardiac event-free survival, older age and underlying cardiopulmonary comorbidities dominated (rather than heart and lung dosimetric parameters) in predicting worse outcome for these patients with preexisting coronary artery disease who later underwent RT.

Conclusions:
Cancer type, older age, and preexisting cardiopulmonary comorbidities and risk factors most significantly predicted clinical outcome and survival for these patients with existing coronary stents who subsequently received thoracic RT. Dosimetric detrimental effects were not significant in our study.
Do Sociodemographic Factors Influence Outcome in Prostate Cancer Patients Treated With External Beam Radiation Therapy?
Authors: Movsas Avielle , Ibrahim Ramy , Elshaikh Mohamed A. , Lamerato Lois , Lu Mei , Sitarik Alexandra , Pradhan Deepak , Walker Eleanor M. , Stricker Hans , Freytag Svend O. , Chetty Indrin J. , Movsas Benjamin , Siddiqui Farzan 
Published: May 2014

Objectives:
The purpose of this study was to analyze the prognostic significance of sociodemographic factors on biochemical control (bNED) and overall survival (OS) in patients with prostate cancer.

Methods:
Prostate cancer patients treated with definitive external beam radiation therapy (EBRT)±hormone therapy from 1997 to 2006 were analyzed in this IRB-approved study. Patient demographics, treatment (Tx), and clinical outcome were obtained from electronic medical records. Median household income (mHHI) at the census block group level was obtained from the 2000 census data. Data on disease and Tx parameters included Gleason score, pre-Tx prostate-specific antigen (PSA), T stage, year of Tx, EBRT dose, and use of hormone therapy. Patients were categorized as having low-risk, intermediate-risk, or high-risk disease. Sociodemographic factors included age, race, marital status, and mHHI. Biochemical failure was defined as nadir PSA+2 ng/mL. OS was based on death from any cause.

Results:
A total of 788 consecutive patients were studied with a median follow-up of 7 years (range, 0.4 to 15 y). African Americans comprised 48% of the patients, whereas 46% of patients were white and 6% were other races. Whites had an average mHHI of $60,190 compared with $36,917 for African Americans (P<0.001). After multivariable modeling, only radiation dose was predictive for bNED (P=0.004) or OS (P=0.008). No sociodemographic factors were predictive for either outcome. Higher radiation dose predicted for better biochemical control and OS.

Conclusions:
This analysis suggests that sociodemographic factors are not important prognostic factors in determining outcome after EBRT for prostate cancer.
Trend in Age and Racial Disparities in the Receipt of Postlumpectomy Radiation Therapy for Stage I Breast Cancer
Authors: Yeboa Debra N. , Xu Xiao , Jones Beth A. , Soulos Pamela , Gross Cary , Yu James B. 
Published: May 2014

Objectives:
Significant effort has been expended over the past decade to reduce racial disparities in breast cancer care. Whether disparities in receipt of appropriate radiotherapy care for breast cancer persisted despite these efforts is unknown, as is the impact of being eligible for Medicare. We therefore investigated trends in racial differences by age in postbreast lumpectomy radiation therapy (PLRT) from 2004 to 2009.

Materials and Methods:
We analyzed the Surveillance, Epidemiology and End Results registry database for women aged 40 to 85 years who underwent lumpectomy for stage I breast cancer and were eligible for PLRT. We examined variables potentially associated with the receipt of PLRT, including year of diagnosis, race, and examined women separately by age group.

Results:
Among 67,124 women aged 40 to 85 years undergoing lumpectomy, receipt of PLRT decreased from 80.7% in 2004 to 76.8% by 2009 (P<0.001). There remained a persistent disparity in PLRT among African American women (in 2004, 80.6% white vs. 78.9% African American and in 2009, 77.5% white vs. 72.0% African American). In multivariable logistic regression, African American race (odds ratio [OR], 0.82; 95% confidence interval [CI]. 0.76-0.89) and being diagnosed more recently were associated with lower odds of PLRT (OR for 2009 vs. 2004: 0.74; 95% CI, 0.69-0.79), whereas older women typically covered by public health insurance (aged 65 to 69 y) were more likely to receive PLRT (OR, 1.09; 95% CI, 1.02-1.15).

Conclusions:
PLRT decreased by a significant percentage of 3.9% among all women in recent years, and racial disparities in PLRT receipt have persisted. Medicare eligibility increased the likelihood of PLRT receipt.
Gender representations in children's media and their influence
Authors: Steyer Isabella 
Published: May 2014

Purpose
– The purpose of this paper is to draw attention to the significant underrepresentation of females and stereotypical portrayals of both females and males that still exist in different kinds of media children are exposed to, as well as to various negative influences these may have on children's development. In addition, this paper intends to show up the potential positive effects of non-sexist gender representations in these media.

Design/methodology/approach
– The paper reviews studies that have been conducted on various kinds of media, in order to gain and provide a representative overview of gender portrayals and of possible influences they might have on children.

Findings
– Women are underrepresented in children's literature, television programs, as well as computer-related software. Traditional portrayals of females are also still the norm in these media that children are daily faced with. Alarming trends regarding the representations of males have also been found. The negative influence of sexist representations on children has been shown by numerous studies, as has been the potential of positively affecting children's development by exposing them to non-traditional gender representations.

Originality/value
– Awareness of how highly present sexism still is in media for children and of the ways in which it may inhibit children's development is seen as a crucial step toward change. Change in this field is needed if we want to ensure a better, more equal future for our world.
Colour consultation with dementia home residents and staff
Authors: Godwin Beatrice 
Published: May 2014

Purpose– Government guidelines promote service user consultation without providing extensive advice on people in later dementia. “Seen as too difficult to involve, they are effectively excluded from […] influenc(ing) service provision”, especially institutional care residents (Clare and Cox, 2003, p. 936). This hard-to-reach group presents methodological challenges. The purpose of this paper is to explore innovative approaches, offering even those with fragmented or lost speech the opportunity to contribute to decisions about their care.Design/methodology/approach– This specialist dementia home consultation included staff and every resident, irrespective of the level of their communication impairment. Consultation on potential colour schemes took the form of a ballot. Staff helped develop an unpatronising, person-centred approach. Visual aids supported communication, de-emphasising the spoken word and promoting inclusion.Findings– The majority of residents appeared to express an opinion on the potential decor. Others chose a colour while not necessarily grasping the context. The approach engaged all except four.Research limitations/implications– Even people with moderate/advanced dementia may be enabled to participate in consultation. Further research needs to refine methodology to include everyone and clarify the interpretation of results.Practical implications– Service providers may widen their expectations of inclusivity in consultation exercises.Originality/value– This consultation is important to researchers and practitioners because it explores ways of communicating, which avoid privileging the spoken word, revealing seldom-recognised abilities in people with moderate/advanced dementia.
Optimization of Extraction of Bioactive Compounds from Different Types of Grape Pomace Produced at Wineries and Distilleries
Authors: Brazinha Carla , Cadima Mafalda , Crespo João G. 
Published: June 2014

AbstractNatural extracts obtained from grape pomace are particularly interesting, due to the substantial variety of valuable compounds present with health benefits, specifically phenolic compounds such as anthocyanins, trans‐resveratrol, quercetin, and proanthocyanidins. The production of such extracts has been recognized as a profitable way to valorize grape byproducts, which are low‐value and most abundant. First, the effect of the solvent on the extraction of bioactive compounds from grape pomace is studied. The selected solvents are water and ethanol, biocompatible and available in wineries and distilleries. Then, different types of grape pomace obtained along the various stages of current industrial winemaking and distillation processes are analyzed. As a result, the best stage of the winemaking and distillation processes for pomace valorization is identified, corresponding to the grape byproduct with the highest potential as source of bioactive compounds. These studies were performed with Vitis vinifera variety of Tempranillo grapes (same year, same vineyard).
Influence of Bacterial Cellulose (nata) on the Physicochemical and Sensory Properties of Frankfurter
Authors: Yu Shih‐Yi , Lin Kuo‐Wei 
Published: June 2014

AbstractThe physicochemical and sensory characteristics of pork frankfurters containing different levels (10% to 30%) of bacterial cellulose (nata) were evaluated. Emulsion stability of the raw meat batter decreased with the addition of nata. For nata‐added treatments, increasing levels of nata in frankfurters resulted in decreased textural hardness and shear values. Sensory results indicated that N10 and N20 had significantly higher firmness scores than N30 and control. However, juiciness score did not differ for all treatments. Incorporation of nata at lower levels (10% to 20%) did not have detrimental effects on the physicochemical, textural, sensory, and microbiological properties of regular‐fat frankfurters. Addition of a higher level (30%) of nata essentially produced comparable sensory properties to the control, but lower levels of nata in frankfurters yielded higher sensory firmness and instrumental hardness values. Based on the composite results, manufacture of regular‐fat frankfurter containing 10% to 20% high‐fiber nata resulted in product quality comparable to the control.
Using modestr to download, import and clean species distribution records
Authors: García‐Roselló Emilio , Guisande Cástor , Heine Juergen , Pelayo‐Villamil Patricia , Manjarrés‐Hernández Ana , González Vilas Luis , González‐Dacosta Jacinto , Vaamonde Antonio , Granado‐Lorencio Carlos 
Published: May 2014

Summary

Data quality is one of the highest priorities for species distribution data warehouses, as well as one of the main concerns of data users. There is the need, however, for computational procedures with the facility to automatically or semi‐automatically identify and correct errors and to seamlessly integrate expert knowledge and automated processes.

New version modestr 2.0 (http://www.ipez.es/ModestR) makes it easy to download occurrence records from the Global Biodiversity Information Facility (GBIF), to import shape files with species range maps such as those available at the website of the International Union for Conservation of Nature (IUCN), to import KML files, to import CSV files with records of the users, to import ESRI ASCII grid probability files generated by distribution modelling software and show the resulting records on a map.

modestr supports five different methods for cleaning the data: (i) data filtering when downloading records from GBIF, (ii) habitat data filtering, (iii) taxonomic disambiguation filtering, (iv) automatic spatial dispersion and environmental layer filters and (v) custom data filtering.
Frequency and intensity of drought stress alters the population size and dynamics of Elatobium abietinum on Sitka spruce
Authors: Banfield‐Zanin J.A. , Leather S.R. 
Published: May 2014

AbstractThe green spruce aphid, Elatobium abietinum, is the most important defoliating pest of Sitka spruce, Picea sitchensis, in the UK. Populations are expected to increase in response to predicted climate change, therefore placing Sitka spruce under increased risk of widespread and severe defoliation. The effect of spring–summer drought stress on E. abietinum population dynamics and development over multiple years was assessed in a field experiment under five different drought treatments with differing intensities and frequencies. The impact on host tolerance, in terms of needle retention, was also investigated. No differences in the length of time taken to reach peak population size were observed. Despite this, E. abietinum populations were found to respond positively to low amplitude intermittent stress, with high densities maintained for longer after the peak. Spring peak densities of aphids did not differ among drought levels, although an autumn peak was observed consistently over 2 years on trees subjected to continuous severe drought. This suggested advancement in the onset of Sitka spruce dormancy. Aphid infestation significantly increased percentage needle loss under all drought treatments, although no differences were observed between drought levels. An interaction between aphid presence and drought treatment was, however, observed during a second year of drought where no aphids were present. The study herein presented has contributed to the understanding of E. abietinum population responses under a changing climate. The implications for damage to host Sitka spruce are of relevance to forest management strategies, as an increase in drought events are predicted in the UK.
Gene profiling reveals association between altered Wnt signaling and loss of T‐cell potential with age in human hematopoietic stem cells
Authors: Khoo Melissa L. M. , Carlin Stephen M. , Lutherborrow Mark A. , Jayaswal Vivek , Ma David D. F. , Moore John J. 
Published: May 2014

SummaryFunctional decline of the hematopoietic system occurs during aging and contributes to clinical consequences, including reduced competence of adaptive immunity and increased incidence of myeloid diseases. This has been linked to aging of the hematopoietic stem cell (HSC) compartment and has implications for clinical hematopoietic cell transplantation as prolonged periods of T‐cell deficiency follow transplantation of adult mobilized peripheral blood (PB), the primary transplant source. Here, we examined the gene expression profiles of young and aged HSCs from human cord blood and adult mobilized PB, respectively, and found that Wnt signaling genes are differentially expressed between young and aged human HSCs, with less activation of Wnt signaling in aged HSCs. Utilizing the OP9‐DL1 in vitro co‐culture system to promote T‐cell development under stable Notch signaling conditions, we found that Wnt signaling activity is important for T‐lineage differentiation. Examination of Wnt signaling components and target gene activation in young and aged human HSCs during T‐lineage differentiation revealed an association between reduced Wnt signal transduction, increasing age, and impaired or delayed T‐cell differentiation. This defect in Wnt signal activation of aged HSCs appeared to occur in the early T‐progenitor cell subset derived during in vitro T‐lineage differentiation. Our results reveal that reduced Wnt signaling activity may play a role in the age‐related intrinsic defects of aged HSCs and early hematopoietic progenitors and suggest that manipulation of this pathway could contribute to the end goal of improving T‐cell generation and immune reconstitution following clinical transplantation.
Does individual experience affect performance during cardiopulmonary resuscitation with additional external distractors?
Authors: Krage R. , Tjon Soei Len L. , Schober P. , Kolenbrander M. , van Groeningen D. , Loer S. A. , Wagner C. , Zwaan L. 
Published: June 2014

SummaryCardiopulmonary resuscitation is perceived as a stressful task. Additional external distractors, such as noise and bystanders, may interfere with crucial tasks and might adversely influence patient outcome. We investigated the effects of external distractors on resuscitation performance of anaesthesia residents and consultants with different levels of experience. Thirty physicians performed two simulated resuscitation scenarios in random order, one scenario without additional distractors (control) and one scenario with additional distractors (noise, scripted family member). Resuscitation performance was assessed by a score based on European Resuscitation Council guidelines, presented as median (IQR [range]). We found that performance scores were lower under experimental conditions (11.8 (9.0–19.5 [−9.0 to 28.5]) than under control conditions 19.5 (14.0–25.5 [5.0–29.5]), p = 0.0002). No interaction was observed between additional distractors and experience level (p = 0.4480). External distractors markedly reduce the quality of cardiopulmonary resuscitation. This suggests that all team members, including senior healthcare providers, require training to improve performance under stressful conditions.